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1. 207 open shell systems energy contributions in output 114 key Wotds iece mereri Optimization folder optimizations see geometry optimization orbital energies in output 114 orbitals COMBINING sessista ansins 238 239 fixing symmetry populations 71 information in output 111 116 keywords for output of 215 218 output options eeeerenee 139 142 plotting iiie ene 84 85 printing for guess section 236 IGOFdetme aren ar a nt 238 239 SUFFACES neigen 84 order of Jaguar programs run SpeCifyInE eee eerie 239 241 ordering of dealiasing functions 251 Jaguar 6 0 User Manual organometallics improving convergence iT 145 146 147 148 output file echoing input file in 239 location 31 32 reference in log file 143 standard output settings 135 138 summarizing eee 105 110 output file information IDASIS Set tecti iE reat 132 convergence methods other than DIIS 135 DFT calculation options 115 frequency IR and thermochemistry calculatioris eee 129 geometry and transition state optimizations andy GVB calculations vee 116 LMP2 calculation options 113 properties 124 solvation calculations 120 Output fol
2. eese 299 SGI installation eee 298 partial charges from ESP fit netten 74 Mulliken 226a 76 path specifying order of programs 239 241 PDE prograli ee 240 output from geometry optimizations 124 per iteration output options 215 216 physical constants and conversion factors keyword osis tete 202 pick states see object types for selection Pipek Mezey localization A in LMP2 calculations cece 64 keywords 179 208 209 orbital printing 140 pK calculations conformational flexibility 313 empirical corrections eees 312 equivalent sites 313 314 geometry optimization eee 310 initial geometry eene 330 input files reto rere tnter 327 THOTUtOTDS nat 329 multiple protonation sites 313 315 326 PUNND E siais iraani ciais 325 328 single point energies eects 311 solvation free energy 311 THEORY 310 pK prediction module 1nstallihg s iid te 325 parameterized functional groups 316 training set results 315 plot data generating sss 84 222 POE Parallel Operating Environment options automatically set 306 version required sese 304 point charges input file section for 236 237 Pois
3. sse 92 for geometry optimization 37 40 90 92 172 188 frozen coordinates ss 91 173 transition state searches nne 96 convergence criteria geometry optimization 89 119 191 SCH enefey a c tte einer terre 69 151 SCF energy keyword 201 solvation energy keyword 195 convergence problems troubleshooting 295 convergence schemes sseseseseeee 70 DIIS ni 10 135 keywords 201 202 OCBSE 52i ReauchUP HEN 70 135 coordinates Cartesian in geometry input 36 constraining and freezing 90 93 for refinement of Hessian 40 98 FEACHON os aede EH WEE 102 192 redundant internal sss 90 um 99 101 Coulomb field charge fitting to 125 Coulomb operator J sssss 203 keyword for output sess 216 obtaining i o information for 136 pseudospectral assembly of 156 157 counterpoise calculations 40 170 171 defining fragments for 233 specifying atoms for 40 233 coupled perturbed Hartree Fock CPHF terms for LMP2 dipole moments 63 76 for LMP2 ESP fitted charges
4. sees 212 transition state 186 killing jobs een 278 L launch host ueeenseenneneenneen 291 292 LDA see Local Density Approximation least squares operator Q description of 155 156 level shiftng 5 onere riti 70 Hessian keyword for s 190 virtual orbitals keyword 204 Lewis dot structure keywords for 176 177 oewrsdleso oue Ae tres 243 setting GVB pairs from 176 177 setting van der Waals radii from 120 195 lewis file description and format 260 268 specifying in input file 167 Linear Synchronous Transit LST methods see QST guided transition state searches LMP2 method 63 65 161 164 key Words ceret mh ibi rnn output from sese pseudospectral implementation S ETIBS S eio re iet e pel ire LMP pairs delocalization of 178 179 225 226 input file section for 178 179 225 226 keywords nennen 178 179 LINO 2 PLO STAIN sesa anann 240 Imp2der program nemen 240 l1mp2dip program scissioni 240 lmp2gda program eseis 240 l1mp2gdb program seeee 240 Output Mom 2er 118 Local Density Approximation LDA 61 164 dftname values for 180 local job directory sse 48 52 local LMP2 method cece eee eee 64 65 grid iiie ede diiit 219
5. 64 74 covalent radii usse 229 cpolar program 240 iin M M 213 Culot Fletcher method for trust radius adjustment key WOT eerte 190 current working directory sess 4 cutotf file 297 259 default nieder n Diretta 243 description and format 257 specifying in input file 167 Index cutoff methods ueeeeee 68 88 202 CUtOTfS rare 203 204 257 259 shown in output oo eects 113 143 D daf file default uino etie 243 description and format u 249 254 neighbor ranges 249 250 specifying in input file 167 dealiasing functions 55 249 choices for calculation 250 contracted 250 251 252 keyword for list in output 212 key words ia treten eniin 218 219 long range eee 249 251 252 neighbor ranges for 137 249 251 ordering of sets cenennnnenennennnnnnnnnn 251 output of number used 212 short range esee 249 251 252 uncontracted sssesseeee 230 251 default atomig file 248 delocalization of LMP pairs 178 225 density difference matrix keyword for output Of 216 RMS of elements in outpu
6. 229 for initial guess 146 235 248 in generated GAUSSIAN input file keyword for list in output keywords listed in output esses utu d dessen polarization functions 55 59 200 244 specifying for GAUSSIAN input 153 215 with ECP in output 132 basis set superposition error 40 63 64 161 batch input file EXAMP sisses een 287 Tormat aine 282 285 batch jobs jaguar batch command for 282 286 IOmol eee ete oro ee a eee 287 running from Maestro 49 51 Gath Sorita ert 282 b ilt iti iieri tert 50 selecting in Maestro 50 BFGS method for Hessian updating keyword 189 BIOGRAF hes files format 234 bond angles freezing all erii 188 freezing for geometry optimization 40 91 92 172 In Z Mal rne oor eta etd 38 output keyword eee 213 bond dissociation assigning GVB pairs for 150 Jaguar 6 0 User Manual 347 Index 348 bond lengths freezingall rnt 188 freezing for geometryoptimization 40 91 92 172 In Z inatfix E 34 output keyword esee 213 bonding types describing in lewis files 261 bonds specifying for internal coordinates 174 Boys localization eene 71 key WOFTdS eet etienne ene 179 208 orbital printing
7. 269 Serate hosii iee 211 283 WOLKIN ned i arl eret creat 283 displacement convergence criteria based on 89 keywords for convergence criteria 191 display host ee 289 291 292 Display Options dialog box 86 dsoly Pro grains ae 240 dummy atoms in charge fitting esses 125 in the Hessiali eite 234 in Z matrix inPUt unsessnesesnenennsnennnnnnnnn 39 dynamic constraints eee 92 173 E Edit Job dialog box sess 34 effective core potentials ECPs basis Sets fot cerco 57 59 in atomic guess file 249 in basis set file hes 245 247 NMR shielding constants 78 eigenvector following in transition state optimiza tions keywords sense 188 option SEIN sisisi siaii 97 use of Hessian refinement 97 eTden program eiecit tees 240 Jaguar 6 0 User Manual 349 Index 350 electric field for polarizability calculations input file section teint 237 KEY WOT n tries 197 SEINE M TI electron density keywords ttt 197 219 keywords for as 288 197 output from calculation 127 SULLACE inier 84 electron density output file 127 197 electrostatic potential ini espfile e te DEF 215 output on a grid ss
8. 167 grid ptrOgrFatm unseren 230 output from 112 118 120 grid shell locations keyword for output of 213 Pu p M 88 CUSTOM eree 168 220 for electrostatic potential iili riy P PNE E 75 76 196 220 grid file eee pepe 167 information in log file 143 information in output 112 113 keywords ner 218 220 selecting DET 4 0 2220 59 shells for in grid file 255 256 specified in cutoff file 258 259 grids pseudospectral accuracy level sess 68 202 basis set availability sss 35 keyWOELdS estere 203 219 220 STOW bond a once dn Bed Hien ee ite tpe 19 Jaguar 6 0 User Manual GVB calculations 66 67 157 161 from HF converged wavefunction 146 206 generating GAUSSIAN input for 152 GVB data output sees HF initial guess eese input HF wave function Keywords een Output from ionmaine etre pair selection tips printing orbitals ssss ITeStarting i c rre nun troubleshooting eene GVB pairs definition iieri 158 heteroatom 66 177 input file section for 224 225 output information 116 117 selection tips 150 setting from Lewis dot structure 176 177 specifying for GAUS
9. eene 213 Murtagh Sargent method keyword 189 N Natural Bond Orbital NBO calculations 20 0 77 129 241 242 neighbor rang s enm erre 250 nice option jaguar run command 276 NMR shielding constants Ia 197 SGItIIBS eie iet periere HERE TA non local ensity approximation NLDA 165 Jaguar 6 0 User Manual 355 Index 356 nude plogfam oec estet 240 number of iterations for geometry convergence maximum ssis iisen 89 149 187 number of processors determining optimum eee 306 Selecting 5 certet ient 276 numeric updating of Hessian keyword 189 numerical gradient of energy 87 keywords het 187 189 numerical Hessian printing in freq output 213 numerical methods 155 157 cutoff file determination of 259 numerical second derivative of energy 79 keywords rtr 189 199 O object types for selection 7 21 OCBSE convergence scheme 70 nee progra RR 239 output from 111 118 120 one electron Hamiltonian keyword for output Of 213 output option eterni tteit 138 one electron integrals sees 111 energy contributions 121 122 online belpas nn E R 28 open shell singlet keyword
10. 182 For instance if idft 1301 the DFT calculation uses the Slater local exchange functional and the Perdew Zunger local correlation functional with Perdew s 1986 non local correlation func tional A typical local density approximation LDA calculation could use idft 101 while idft 2011 sets the popular NLDA choice called BLYP If you specify the Lee Yang Parr func tional which contains local and non local terms you may not specify a local correlation func tional i e if j 2 k must be 0 unless you are using the Becke 3 parameter hybrid method as described below Table 9 10 Values of m in idft where idft ijkim m in idft Local Exchange Functional or Exact Exchange m 0 exact exchange Hartree Fock m 1 Slater m 9 Xa Table 9 11 Values of I in idft where idft ijkim lin idft Non local Exchange Functional I 0 none I 1 Becke 1988 nonlocal term only I 3 Becke 1998 B98 nonlocal exchange functional I 4 Perdew Wang GGA I 1991 nonlocal exchange only I 6 Schmider and Becke 1998 SB98 nonlocal exchange functional I 7 HCTH407 nonlocal exchange functional I 8 B97 1 nonlocal exchange functional I 9 PBE nonlocal exchange functional Table 9 12 Values of k in idft where idft ijkIm k in idft Local Correlation Functional k 0 none k 1 Vosko Nusair Wilk VWN k 2 VWNS k 3 Perdew Zunger 1981 k 4 Perdew Wang GGA II 1991 local correlation only Jaguar 6 0 User Manual Chapter 9 The Jaguar In
11. Product Q aldehyde Choose Number of IRC points 6 IRC step size 0 10 Maximum optimization steps per point 30 _ Use mass weighted coordinates Job Start Read Write Edit Reset Close Help Figure 5 4 The IRC folder Quantum mechanical Do not use any of the other options from this menu because it is important to have an accurate Hessian If you precalculate the Hessian and read it in the symmetry of the transition state is used for the entire calculation If the IRC path breaks symmetry you should turn symmetry off in the Molecule folder If you calculate the Hessian as part of the IRC or MEP calculation symmetry is turned off in the Hessian evaluation and remains off for the remainder of the run IRC and MEP calculations can be run in either direction from the transition state You can select the direction of the scan from the Direction option menu The direction of the reaction 30 Keyword inhess 4 in the gen section Jaguar 6 0 User Manual 103 Chapter 5 Optimizations and Scans 104 coordinate can be defined by supplying the reactant structure and the product structure in the Structures section of the IRC folder These geometries are selected in the same way as for a transition state search see Section 5 3 2 on page 95 The same rules for atom numbering in the reactant and product structures apply as for transition state searches If you do not supply the
12. and g are the matrix elements F and F in the localized molecular orbital basis and and are the eigenvalues of the Fock matrix in the local virtual basis From the C as va and the exchange matrices K Jaguar computes the second order energy cdiotion E from the equations E K C 17a i2j C 1 8 4G 2C 17b where the bracket in Equation 17a denotes a trace and 8 is 1 if i j and O otherwise Computing the exchange matrix elements for Equation 17a is approximately 80 of the work for an energy correction computation while generating the C coefficients comprises about 20 of the work Jaguar performs localized MP2 calculations using pseudospectral methods evaluating inte grals over grid points in physical space in a manner similar to that described for HF and GVB calculations in Section 8 1 on page 155 and Section 8 2 on page 157 The two electron exchange integrals needed for Equation 17a are evaluated over grid points g as follows Pq Kj 2 0 jag pg 18 where Q is the least squares fitting operator for molecular orbital i on grid point g R is the physical space representation of virtual orbital p and A is the three center one ln inte gral over the occupied molecular orbital j and the local virtual orbital q The last term is related to the three center one electron integrals in atomic orbital space A described in Equation 2 by Ajgg D Cy IgA ug 19 kl The summatio
13. elements is less than the RMS density matrix element change criterion whose default value is 5 0 x 10 The SCF calculations during an optimization to a minimum energy structure or transition state do not use the energy convergence criterion used by other SCF calculations The RMS density matrix element criterion may be set in the SCF folder The geometry is considered to have converged when the energy of successive geometries and the elements of the analytic gradient of the energy and the displacement have met the conver gence criteria These criteria are all affected by the choices in the Convergence criteria section Default or Loose the loose criteria are all five times larger than the default criteria For opti mizations in solution the default criteria are multiplied by a factor of three and a higher priority is given to the energy convergence criterion Thus if the energy change criterion is met before the gradient and displacement criteria have been met the geometry is considered converged See Section 9 5 9 on page 186 for details on the geometry optimization conver gence criteria or information on how to edit the input file to set them directly In case the optimization process does not converge you can set an upper limit on the number of steps taken by entering a value in the Maximum steps text box The default is 100 Many cases will meet the convergence criteria after ten or fewer geometries are computed However inpu
14. 32 3 2 The Jaguar Panel The Jaguar panel is the main interface between Maestro and Jaguar In this panel you can set up input files for a range of Jaguar jobs and start the jobs To open the panel choose the task or calculation type from the Jaguar submenu of the Applications menu in the main window The available tasks are Single Point Energy Optimization Relaxed Coordinate Scan Rigid Coordinate Scan Transition State Search Reaction Coordinate Initial Guess Only Below these tasks in the menu are two calculation types that are run as Jaguar batch jobs pKa e J2 The input for these calculations is described in this chapter and Chapter 14 Most of the Jaguar panel is occupied by a set of tabbed folders in which you can make settings for jobs These folders are described in Chapter 4 At the top of the panel is a section for selecting the source of job input The Use structures from option menu has three choices e Workspace included entries the structures that are displayed in the Workspace e Selected entries the structures that are selected in the Project Table These need not be the same as the included entries Selected structure files the structures that are in the files listed in the Files text box You can navigate to the desired files using the Browse button When you click OK in the file selector that is displayed the file name is added to the list in the Files text box If you
15. Adamo C Barone V J Chem Phys 1998 108 664 Lynch B J Fast P L Harris M Truhlar D G J Phys Chem A 2000 104 4811 Xu X Goddard W A III Proc Natl Acad Sci U S A 2004 101 2673 Meller C Plesset M S Phys Rev 1934 46 618 S b S Pulay P Theor Chim Acta 1986 69 357 Sebg S Pulay P Ann Rev Phys Chem 1993 44 213 S b S Tong W Pulay P J Chem Phys 1993 98 2170 Foster J M Boys S F Rev Mod Phys 1960 32 300 Pipek J Mezey P G J Chem Phys 1989 90 4916 Harding L B Goddard W A III J Am Chem Soc 1975 97 6293 Carter E A Goddard W A III J Chem Phys 1987 86 862 Fischer T H Alml f J J Phys Chem 1992 96 9768 Schlegel H B Theor Chim Acta 1984 66 333 CRC Handbook of Chemistry and Physics Weast R C Ed 60th edition CRC Press Boca Raton FL 1979 Dielectric constants for 20 deg C were used Water s probe radius is set to 1 40 to reproduce solvation energies properly All other probe radii are calculated from r 3mA 4np 10 A cm where r is the solvent probe radius in Angstroms m is the molecular mass obtained by dividing the molecular weight given in ref 55 in grams per mole by 6 02 x 10 A is the packing density and p is the density in g cm at 20 deg C obtained from ref 55 Finding the actual A would require a detailed knowledge of the structure of the liquid Current
16. The information in the gau file depends on the information you have provided The file always contains a molecular geometry in Cartesian coordinates and angstroms instructions for how to input geometries are available in Section 3 4 on page 35 The file also specifies the molecular charge and the spin multiplicity of the molecule If you want either of these values to be non zero you can make the appropriate settings in the Molecule folder You can also set the name of the basis set you want to provide in the gau file for example STO 3G using the Molecule folder The default basis set choice is 6 31G To actually generate the gau file you need to run the Jaguar job you have just specified See Section 3 9 on page 46 for information on running jobs 76 1 Making Input Files for GVB Calculations To set up the gau file for a GVB calculation you should specify the GVB pairs in the Theory folder See Section 4 6 on page 66 for information on setting up GVB calculations If you have selected a GVB calculation symmetry is automatically turned off and the gau file also specifies nosymm You might want to delete this setting from the gau file after it is produced The gau file also contains a Jaguar generated initial guess if you have selected a GVB calcu lation and notes that this trial wave function is to be used as an initial guess for the GAUSSIAN run guess cards If you have chosen to do an initial guess only calculat
17. character at the beginning of the path Table 9 47 gives a brief description of each Jaguar program Table 9 47 Individual programs included in Jaguar Program Description jexec Driver program for all Jaguar executables note inclusion of jexec in path will cause recursive Jaguar calculations pre Reads and checks input including path if any performs symmetry analysis and calculates terms dependent on geometry e g nuclear repulsion energy onee Calculates one electron integrals and effective core potential ECP contribution to one electron Hamiltonian when relevant hfig Calculates Hartree Fock initial guess probe Insures orthogonalization grid Generates grids rwr Generates Q operators Jaguar 6 0 User Manual 239 Chapter 9 The Jaguar Input File 240 Table 9 47 Individual programs included in Jaguar Continued Program Description gvbig Calculates GVB initial guess scf Performs self consistent field calculation ch Evaluates electrostatic properties multipole moments electrostatic potential fit ting Mulliken populations lmp2dip Calculates dipole moments for LMP2 wave functions cpolar Finds polarizabilities and hyperpolarizabilities using coupled perturbed HF method polar Finds polarizabilities and hyperpolarizabilities using finite field method elden Calculates electron density on set of grid points local Performs localization of orbitals lmp2 Performs local second order Meller Pless
18. Display a version of the Property menu Right click in the column header for a property Edit the text or the value in a table cell Click in the cell and edit the text or value Include an entry in the Workspace Click the In column of the entry exclude all others Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Table 2 3 Mouse operations in the Project Table Continued Task Mouse Operation Move selected entries Paste text into a table cell Resize rows or columns Select an entry deselect all others Select or include multiple entries Toggle the selection or inclusion state 2 4 6 Drag the entries Middle click Drag the boundary with the middle mouse button For an unselected entry click anywhere in the row except the In column for a selected entry click the row number Click the first entry then shift click the last entry Control click the entry or the In column Project Table Shortcut Keys Some frequently used project operations have been assigned shortcut key combinations The shortcuts their functions and their menu equivalents are listed in Table 2 4 Table 2 4 Shortcut keys in the Project Table Keys Action Equivalent Menu Choices CTRL A Select all entries Select gt All CTRL F Fix entry in Workspace Entry gt Fix CTRL I Open Import panel Table gt Import Structures CTRL N Include only selected entries Entry gt Include Only CTRL U Deselect all entries Select gt
19. Finally the iq keywords allow you to choose when to compute the full least squares fitting matrix Q from the smaller matrix S R wR and whether to store it on disk Names and default values in bold italics for these keywords are indicated in Table 9 40 If a grid is used only once per calculation as the fine ultrafine and gradient grids generally are setting its igname value to 0 saves disk space and costs no CPU time Setting the iqname values for other grids to 0 adds some CPU cost but saves some disk space Note If you set iqgrad you must set iqufine to the same value 220 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 39 Keywords related to memory and disk use Keyword Default Description mxstrip 200 Information for matrix elements evaluated on basis functions stored in core in strips of mxstrip N words rather than N words at a time where N is the number of basis functions mxpage 1000 For pseudospectral evaluation of J and K on grid points in pro gram scf memory is allocated ngblok mxpage words at a time as needed where ngblok is a parameter currently set to 128 nbuck 64 Grid blocks are split up into subblocks whose points are all on the same atom and in the same region of space with at most nbuck points where nbuck lt ngblok ngblok is the maximum number of grid points per grid block currently set to 128 nbcmax 1000000 Maximum memory i
20. Keyword Prints Orbitals ip100 For initial guess from before SCF generally redundant with ip105 ip101 In canonical orbital space each SCF iteration ip102 At end of job ip103 In atomic orbital space each SCF iteration ip104 In atomic orbital space after SCF Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 35 Keywords that specify when to print orbitals Continued Keyword Prints Orbitals ip105 For HF initial guess ip106 For GVB initial guess ip107 After Boys or Pipek localization Table 9 36 explains the possible values for the orbital output options aside from 1 the default which turns off printing The variable n in the table can be either 0 5 or 10 If it is 0 all occu pied orbitals including GVB natural orbitals are printed If n is 5 all occupied orbitals and ipvirt virtual orbitals are printed or all virtuals if ipvirt 1 Setting n to 10 causes only the GVB non orthogonal orbitals to be printed Table 9 36 Dependence of the format and type of orbital output on the value ofipx Value of ipx 24n 34n 44n 5 n 6 n Format f5 2 f10 5 f19 15 f8 5 e15 6 Atom basis function type Y Y N N N shown Orbital occupation indicated Y N Y Y N Coefficients printed large all all all all Form shown list table list list table a The value of n determines which orbitals e g occupied are printed x determines the stage at which orbitals are printed see Table 9 35 For example ip106 10 mean
21. n Xi Ar X cosp x sinB Note that an angle of 90 permutes the two orbitals reversing the sign of one Each combination operation is performed independently and the operations are performed in the order they are listed in the orbman section Each rotation involving a previously altered orbital uses the new transformed orbital generated by the earlier operations After all manipu lations have been specified the word end should be included Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File For UHF wave functions the syntax is modified slightly and the alpha and beta spin orbitals are designated by hfiglcmoa and hfiglcmob amp orbman hfiglcmoa hfiglcmob amp i j amp k 1 B end qd Y r S 6 end 9 15 The echo Section The echo section contains only its own label and requests a copy of the input file to be printed in the output file amp echo amp 9 16 The path Section The path section allows you to specify the execution path which determines the order of the Jaguar or other programs to be run If no path section exists Jaguar will use the default path resulting from the settings in other sections of the input file The items listed in a path can be either Jaguar programs UNIX commands or other programs accessible from the executable directory If a program or command is not accessible from the executable directory you must specify the full path for that program with a
22. 267 Chapter 10 Other Jaguar Files 268 desired for the molecule the keyword lewstr should be changed to correspond to a better structure as described in Section 9 5 on page 174 To avoid using Lewis dot structures for either correction terms or radius settings set the gen section keyword isurf to 0 To use Lewis dot structures to set radii but not for correction terms isurf should be 0 but the keyword ivanset should be 1 All Lewis dot keywords are explained in Section 9 5 5 on page 176 The radius settings in the file default lewis which appears in the standard data directory were optimized for HF GVB and LMP2 solvation calculations in water with Jaguar s solva tion module that included the default correction terms for the cavity and surface area The molecules used for radius optimization were the molecules containing carbon hydrogen oxygen nitrogen and sulfur from reference 140 AII calculations used a 6 31G basis set Geometries were obtained from gas phase optimizations at the HF GVB and LMP2 levels For both the geometry optimizations and the solvation energy calculations the GVB and LMP 2 treatment was restricted to heteroatom pairs Jaguar 6 0 User Manual Chapter 11 Running Jobs Running monitoring and controlling jobs is done by the Maestro job control facility This facility has both a graphical user interface in the Maestro Monitor panel and a command line interface in the jobcontrol command The jo
23. 69 Keyword gcharge 1 in the gen section 70 Keyword gcharge 2 in the gen section Jaguar 6 0 User Manual 75 Chapter 4 Options 76 discarded The van der Waals surface used for this purpose is constructed using DREIDING 60 van der Waals radii for hydrogen and for carbon through argon and universal force field 57 van der Waals radii for all other elements These radii are listed in Table 9 43 The radius settings can be altered by making vdw settings in the atomic section of an input file as described in Section 9 8 on page 226 You can also print out the values of the electrostatic potential at grid points whose locations you specify See Section 9 5 13 on page 196 4 10 2 Mulliken Population Analysis Mulliken populations 61 can be computed for each atom giving a representation of the mole cule as a set of nuclear centered point charges For open shell cases Mulliken spin popula tions are also computed when Mulliken populations are requested If you choose to calculate both Mulliken populations and multipole moments the multipole moments are computed from the atomic Mulliken populations as well as from the wave function Mulliken populations can be computed for each basis function as well as for each atom or for each bond between neighboring atoms as well as by atom and basis function by choosing the appropriate option in the Method section 4 10 3 Multipole Moments Jaguar can compute multip
24. Chapter 13 Parallel Jaguar 13 1 2 LINUX Installation For Linux parallel Jaguar requires the MPICH package Jaguar is now supported under Red Hat Linux 7 3 which is based on a Linux 2 4 kernel Earlier versions might run but are not supported If Jaguar is to run in parallel on a multiprocessor machine the kernel must be compiled for SMP symmetric multiprocessing 13 1 2 1 Installing MPICH We recommend building MPICH from the source code The latest source code is always avail able from http www unix mcs anl gov mpi mpich Instructions for building and installing MPICH are included with the source code When you build MPICH from the source code include the following configure option with device ch_p4 The directory in which you installed MPICH is referred to below as MPICH_install 13 1 2 2 Configuration 1 Add the MPICH bin directory to the PATH environment variable This is necessary for Jaguar to find the mpirun launch script csh tcsh setenv PATH MPICH_install bin PATH sh ksh bash export PATH MPICH_install bin PATH 2 Edit the file MPICH_install share machines LINUX and list the names of the hosts available for parallel calculations Each line of this file should specify the name of a host and the number of processors on that host separated by a colon The host name should match the output of the hostname command For example homer mynet edu 2 marge mynet edu 2 bart mynet edu 1 3 Edit the
25. Ifthe jobname 1og file contains the error message error while loading shared libraries libhdf5 so cannot open shared object file No such file or directory Jaguar 6 0 User Manual 303 Chapter 13 Parallel Jaguar 304 then SCHRODINGER is not set on at least one of the nodes The serv p4 process transports the environment variables including SCHRODINGER to all job nodes If serv p4 is not running or if it is using the wrong communication port which must match your MPI PASSPORT value or if MPI USEPASSPORT is not set or is misspelled then SCHRODINGER is not set correctly and this error message results If you see the following error message p4 error Child process exited while making connection to remote process on hostname this could be due to the environment variable HOME having a value on the compute nodes different from that on the launch node MPICH s secure server serv p4 checks the file SHOME server apps on the compute nodes to see if the path to the current executable is present If not the executable is not launched The script MPICH bin mpirun ch_p4 is responsible for ensuring that all executables to be launched with mpirun are listed in the file SHOME server apps However mpirun ch p4 only runs on the launch node Thus if HOME is defined differently on the launch and compute nodes the launch node will not update the file that the compute nodes will use If HOME cannot be defi
26. Jaguar 6 0 User Manual 53 Chapter 4 Options Jaguar jaguar Eeki Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Symmetry Use if present Molecular state yy Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge jo Spin multiplicity 25 1 1 Basis set 6 31G Polarization 4 Diffuse None Number of D functions w 5D 6D 120 basis functions Start Read Write Edit Reset Close Help Figure 4 1 The Molecule folder the Symmetry option menu For information on how to make sure the symmetry of your input structure is treated as you expect see Section 3 7 2 on page 44 For some calculations including GVB LMP2 GVB LMP2 calculations and calculations of IR intensities or hyperpolarizabilities symmetry is not implemented and is disabled automatically during the job 1 Keyword isymm 8 in the gen section 2 Keyword isymm 8 and idoabe 1 in the gen section 3 Keyword isymm 0 in the gen section Jaguar 6 0 User Manual Chapter 4 Options 4 2 Basis Sets In the lower part of the Molecule folder you can choose a basis set from the three option menus labeled Basis Set Polarization and Diffuse The Basis Set option menu provides access to all the basis sets available to Jaguar If an option or menu is dimmed it is incompatible wit
27. PARAM P Jaguar 6 0 User Manual 89 Chapter 5 Optimizations and Scans 90 Hessian 54 or the unit matrix For most cases the Schlegel or Fischer Alml f options are the best choices The Schlegel guess is the default The final option Quantum mechanical is to have Jaguar compute the initial Hessian This calculation is the most time consuming of the initial Hessian options Theoretically it is the best option for cases where the other Hessian choices are inadequate although in practical terms other steps taken to improve optimizations are likely to be more cost effective 5 1 3 Coordinate Systems The coordinate system you choose for optimization can have a substantial impact on the convergence of the optimization The ideal set of coordinates is one in which the energy change along each coordinate is maximized and the coupling between coordinates is mini mized The default coordinate system used by Jaguar is redundant internal coordinates In most cases this set of coordinates proves to be the most efficient There are cases where geometry optimizations with this set can fail One example is when a group of atoms becomes collinear and the internal coordinates become ill defined When this happens Jaguar chooses a new set of redundant internal coordinates If this process fails you can restart the optimization with a different choice of coordinates Jaguar provides two other coordinate systems which are ava
28. Status bar displays information about a particular atom or about structures in the Workspace depending on where the cursor pauses e Atom displays the chain residue number element PDB atom name formal charge and title or entry name this last field is set by choosing Preferences from the Maestro menu and selecting the Feedback folder Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Workspace displays the number of atoms entries residues chains and mole cules in the Workspace Clipping planes window displays a small top view of the Workspace and shows the clipping planes and viewing volume indicators Sequence viewer shows the sequences for proteins displayed in the Workspace Command input area provides a place to enter Maestro commands When a distinction between components in the main window and those in other panels is needed the term main is applied to the main window components e g main toolbar 2 3 1 The Menu Bar The menus on the main menu bar provide access to panels allow you to execute commands and control the appearance of the Workspace The main menus are as follows Maestro save or print images in the Workspace execute system commands save or load a panel layout set preferences set up Maestro command aliases and quit Maestro Project open and close projects import and export structures make a snapshot and annotate a project These actions can also be
29. You can change directories by entering the following command in the command input area see page 6 of the main window cd directory name where directory name is either a full path or a relative path 2 3 The Maestro Main Window The Maestro main window is shown in Figure 2 1 on page 5 The main window components are listed below The following components are always visible Title bar displays the Maestro version the project name if there is one and the current working directory Auto Help automatically displays context sensitive help Menu bar provides access to panels Workspace displays molecular structures The following components can be displayed or hidden by choosing the component from the Display menu Your choice of which main window components are displayed is persistent between Maestro sessions Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Title bar Menu bar Workspace 1aestro zone1 dyall Maestro version 5 5 004 Maestro Project Edit Display Tools Applications Toolbar 4 Atoms 39 39 Entries 1 Res 2 Chn 1 Mol 1 Chg Auto Help text area Viewing volume indicator Sequence viewer Status bar Command input area Clipping plane Figure 2 1 The Maestro main window Toolbar contains buttons for many common tasks and provides tools for displaying and manipulating structures as well as organizing the Workspace
30. atomic Sets atom specific properties including atomic masses for isotopes van der Waals radii for solvation calculations and basis functions for individual atoms hess Allows input of initial nuclear Hessian guess Allows input of initial wave function pointch Adds independent point charges efields Adds electric field or fields ham Allows user input of Hamiltonian orbman Allows orbitals to be reordered or linearly combined echo One word section indicating that the input file should be echoed in the output file path Specifies execution path listing order of Jaguar programs to be run nbo Requests NBO Natural Bond Orbital calculation core Specifies SCORE keylist for NBO calculation choose Specifies SCHOOSE keylist for NBO calculation nrtstr Specifies SNRTSTR keylist for NBO calculation amp gen iguess 0 molchg 1 amp sets the iguess and molchg keywords of the gen section to 0 and 1 respectively Sections may span multiple lines and more than one section may appear in a line However a gen section keyword and its value must be on the same line The following example is interpreted in the same way as the gen section example given above Jaguar 6 0 User Manual 169 Chapter 9 The Jaguar Input File 170 This is a comment amp gen iguess 0 molchg 1 amp This is also a comment 9 2 The zmat zmat2 and zmat3 Sections The molecular geometry must be described in the zmat section Details on ente
31. fying basis sets which are included in Jaguar but not in GAUSSIAN Setting ip160 to 4 allows you to include both the initial guess and the basis set in the gau file 7 6 3 Writing Orbitals for GAUSSIAN You can write orbitals from Jaguar in the format used by GAUSSIAN for its guess cards option by choosing to print the appropriate orbitals from the Output folder which is described in Section 6 6 on page 139 You must choose the f19 15 or f8 5 format from the Format option menu Jaguar 6 0 User Manual 153 Chapter 7 Using Jaguar 154 Jaguar 6 0 User Manual Chapter 8 Theory This chapter contains a description of some of the theory behind the methods used in Jaguar Section 8 1 describes the pseudospectral method itself Section 8 2 and Section 8 3 describe GVB and LMP2 calculations and how the pseudospectral method improves computational scaling and efficiency for these methods Section 8 4 contains a brief description of density functional theory Chapter 4 includes information about performing Jaguar calculations using the techniques described here 8 1 The Pseudospectral Method Like conventional ab initio electronic structure codes Jaguar solves the Schr dinger equation iteratively using self consistent field methods to calculate the lowest energy wave function within the space spanned by the selected basis set For calculations on large molecules both conventional and pseudospectral techniques must recalcu
32. 11 1 Customizing Host Configurations sse 269 11 1 4 Thenane And Hes te Sell Sus tr ei ae 271 114 2 The user Selling eng 271 114 3 The Empdur Setting iier tiet citt sott aaa 271 11 4 The groeessors Seg usce PR RUF E een 272 11 2 The jaguar Command cuu eicere estie ia Diete Go esta 11 2 1 Selecting an Execution Host 11 2 2 Selecting Particular Jaguar Executables eene 275 11 2 3 Running a Jaguar Job From the Command Line essesssss 275 11 24 Kling Jaguar JOD cic reb pr Te t i P Pte PER 278 11 2 5 Gonverting Fil amp FOrtmals etie ieri nennen 278 Jaguar 6 0 User Manual Contents 11 3 Running Multiple Jobs jaguar batch eee 282 Ti1 3 1 Batch Input File Format eio itii ke 282 111 3 2 Running Jaguar babeo o cr ee 285 11 3 3 Batch Input File EXamples uses 287 11 3 3 1 Pipelined JODS 287 11 3 3 2 Running Jobs from Input in a Specified Directory 288 Chapter 12 Trogbleshob usan iai tod ER EDS RAS SRM EHE 289 12 1 Problems Getting Started sse 289 12 1 1 The SCHRODINGER Environment Variable eese 289 12 1 2 Including the jaguar Command in Your Path ssssssssss 290 121 3 Problems Starting Ma6SIIO iiic rcs nennen anne 291 12 1 4 Problems Related to Your Temporary Directory es
33. 20 55693 A1 1 34635 A1 0 71380 B2 0 56828 A1 0 49745 B1 0 21516 A1 0 30862 B2 1 01720 B2 1 09266 A1 1 13459 A1 1 16904 B1 1 29575 B2 1 41126 A1 1 80256 A2 1 82999 A1 end of program scf The output from the program scf begins with a list of information detailing various numbers of electrons orbitals Hamiltonians used for the calculation shells and the calculation type Next the energy output from the SCF iterations is shown in table form Some of the text for the column headings should be read down rather than across The number of the iteration is provided first in each row followed by a Y or N indicating whether the Fock matrix was updated or not When the Fock matrix is updated the changes are made using a difference density matrix whose elements reflect the changes in the density matrix elements from the previous iteration to the current one The next entry indicates whether the DIIS convergence scheme was used for that iteration As above Y or N indicate yes or no The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that iteration DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this column reads A it indicates that DIIS was not used for that iteration but the density matrix was averaged The cutoff set for each iteration is indicate
34. At end of job Print the orbitals at the end of the job After HF initial guess Print orbitals used for the HF initial guess 14 Keyword ip168 2 in the gen section 15 Keyword ip165 3 in the gen section 16 Keyword ip175 2 in the gen section 17 Keyword ip102 in the gen section 18 Keyword ip105 in the gen section Jaguar 6 0 User Manual 139 Chapter 6 Output 140 After SCF Print orbitals in atomic orbital space after the SCF converges After final localization Print orbitals after the localization procedure if Boys or Pipek Mezey localization of the wave function has been requested Each iteration in CO space Print orbitals after each SCF iteration in canonical orbital space Canonical orbital eigenvectors with very small eigenvalues are removed from the calculation before the SCF process The number of orbitals printed depends on whether five or six d functions are specified for the basis set as described in Section 4 2 on page 55 Each iteration in AO space Print orbitals after each SCF iteration in atomic orbital space By default no orbitals are printed in the output file so None is selected by default in the Orbitals option menu If you select Occupied orbitals all occupied orbitals including GVB natural orbitals are printed If the All orbitals option is selected all occupied orbitals and ten virtual orbitals are printed To change the default of t
35. Chapter 10 Other Jaguar Files All six integer values and a corresponding radius value must always be listed in an atom type description line and the atomic number must correspond to an actual element However any or all of the other five integer values can be set to 1 a wild card entry indicating that any value for that characteristic matches that atom type description To reset a default radius for hydrogen for instance you could put the following line before any other descriptions of hydrogen atoms 1 1 1 1 1 1 1 10 H all 1 1 ignoring chemical environment and the van der Waals radius for all hydrogen atoms would be set to 1 10 To describe the hybridization of the atom itself the atom type description line s second integer should take on one of the values indicated in Table 10 3 Table 10 3 Lewis file hybridization numbers and corresponding hybridization types Hybridization Corresponding Number Hybridization Type 1 s hybridization p hybridization d hybridization sp hybridization sp hybridization sp hybridization sp d hybridization NO wan QN tA WY N sp d hybridization The description of the atom s bonding type uses the groups listed in the bonding type informa tion described in Section 10 6 1 on page 261 unless it is 1 Any positive integer for bonding type describes the number of bonds the atom has in each of the bonding type groups for its element and or the number of all other bonds the a
36. It is very important to choose the lowest energy conformer for the pK calculations As ab initio geometry optimizers only find the local minima for flexible systems long n alkyl chains many rotatable bonds we strongly suggest first running a conformational search with MacroModel for example to determine the global minimum energy structure which can then be used as an initial structure for the pK run For some systems the protonated and deprotonated structures can adopt different conforma tions in the lowest energy state For such cases you should create Jaguar input files for both structures and use the deprot option of the jaguar pka command to specify the deproto nated structure Output files and results are in the same format as in the single initial geometry runs 14 5 Developing Your Own pK Correction Parameters If you want to develop your own pK parameters you can do so by adding information to the file that contains the parameters that Jaguar uses to correct its calculated pK values S SCHRODINGER jaguar vversion data pka match xml This file also contains the SMARTS patterns that enable Jaguar to recognize functional groups You can thus extend Jaguar s ability to calculate pK values for new functional groups simply by adding the appro priate SMARTS patterns and correction parameters to this file A description of the XML file format standard is beyond the scope of this document but the format is very simple and resem
37. J B Schleyer P von R Binkley J S Pople J A J Chem Phys 1976 64 5142 Binkley J S Pople J A Hehre W J J Am Chem Soc 1980 102 939 Gordon M S Binkley J S Pople J A Pietro W J Hehre W J J Am Chem Soc 1982 104 27797 Pietro W J Francl M M Hehre W J DeFrees D J Pople J A Binkley J S J Am Chem Soc 1982 104 5039 Pulay P Fogarasi G Pang F Boggs J E J Am Chem Soc 1979 101 2550 Dill J D Pople J A J Chem Phys 1975 62 2921 Ditchfield R Hehre W J Pople J A J Chem Phys 1971 54 724 Hehre W J Pople J A J Chem Phys 1972 56 4233 Binkley J S Pople J A J Chem Phys 1977 66 879 Hariharan P C Pople J A Theor Chim Acta 1973 28 213 Hehre W J Ditchfield R Pople J A J Chem Phys 1972 56 2257 Francl M M Pietro W J Hehre W J Binkley J S Gordon M S DeFrees D J Pople J A J Chem Phys 1982 77 3654 Rassolov V A Pople J A Ratner M A Windus T L J Chem Phys 1998 109 1223 Jaguar 6 0 User Manual 339 References 340 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 Clark T Chandrasekhar J Spitznagel G W Schleyer P von R J Comput Chem 1983 4 294 Frisch M J Pople J A Binkley J S J Chem Phys 1984 80 3265 Kri
38. LAV3D LACVP or LACVD or any variant of these sets involving polarization or diffusion functions such as 6 31G the initial guess is formed from wave functions obtained from atomic calculations in that basis set ignoring polarization and diffusion functions Therefore if you change the basis file you need to change the atomig file correspondingly and vice versa For other basis sets the wave functions used to construct the initial guess are obtained by projecting the appropriate atomic wave function in default atomig onto the basis set actu ally being used for the molecular calculation The 6 31G wave function is used whenever possible when a 6 31G atomic wave function is not listed for a particular atom the MSV wave function is used for that atom For atoms beyond Xe in calculations using the LAV 1S basis set the LAV2P atomic results are used As in the default basis file the basis sets listed in the default atomig file are listed in turn and for each basis the information for each atom is listed Each basis set section begins with a blank line which is followed by one or more lines reading BASIS followed by one Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files space and ending with the name or names separated by a space and or comma of all basis sets for which the atomic calculations listed immediately after that line apply The basis set names are listed in Table 4 1 on page 56 and Table 4 2 on page 58 Next
39. Molecule Theory scr Properties Salvation Output Solvent None m Dielectric constant 0 000 Molecular weight 0 00 g mol Density 0 00000 g mL Probe radius 0 00 4 Gas phase reference energy Optimized gas phase structure wv Input structure wv Value 0 00 Job GVB LMP2 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 4 6 The Solvation folder tion incorporating the solvent charges This process is repeated until self consistency is obtained The cost is roughly twice that of a gas phase calculation Solvation energies can be computed with HF DFT GVB or LMP2 wave functions For GVB or local LMP2 solvation energy calculations we recommend using heteroatom pairs for the most efficient results particularly since solvation energy calculations often use radii optimized for calculations that use heteroatom pairs See Section 10 6 on page 260 for more details See Section 4 5 on page 63 and Section 4 6 on page 66 for information on setting LMP2 or GVB pairs Jaguar 6 0 User Manual Chapter 4 Options Solvent parameters are set in the Solvation folder You can choose a solvent from the Solvent option menu and Jaguar performs a solvation calculation setting the appropriate dielectric constant and probe radius The dielectric constant 55 and probe radius 56 values set by Jaguar for various solvents are shown in Table 4 3 Table 4 3 Parameters f
40. Y C QJ qg pu Rus pu 13c q p N yb 2 Y ER 2 qu pu Kye pu q p 1 p _yp _l Ypg pu P ge 2 pg pu 13d In practice since the CI coefficients are mutually interdependent they are determined using a self consistent iterative procedure Jaguar 6 0 User Manual Chapter 8 Theory Next holding the CI coefficients fixed the program evaluates the energy and the Fock matrix and adjusts the basis set coefficients describing the GVB natural orbitals accordingly in basi cally the same manner used for the usual HF treatment The revised orbitals and CI coefficients are then used in the next SCF iteration and the process continues until both the GVB natural orbitals and the CI coefficients have converged The GVB treatment can also be applied to open shell cases or restricted to certain electron pairs These variations are described in Ref 20 which also provides much more detail about the GVB methods and equations The ability to restrict the use of GVB to particular electron pairs is an important strength of the method This feature allows computationally inexpensive correlation of critical regions in very large molecules 8 3 Pseudospectral Local MP2 Techniques Second order Moller Plesset perturbation theory MP2 is perhaps the most widely used ab initio electron correlation methodology recovering a large fraction of the correlation energy at a relatively low computational cost The method greatly improves Hartree Fock treat
41. You should add a single line for each fragment with a formal charge or a non singlet spin multi plicity The first entry in the line under the heading atom should be the atom label of any atom in the fragment The next entry under the heading formal and separated from the first entry by one or more spaces should be the formal charge of the entire fragment The third entry under the heading multip should be the spin multiplicity of the fragment If C1 is in one ring of ferrocene and C6 is in the other ring then the following atomic section could be used to help generate the initial guess atom formal multip Fe 2 1 C1 1 1 C6 1 m amp Fragments with no formal charge and singlet spin water for example do not need to be listed in the atomic section because Jaguar assumes a default formal charge of 0 and multiplicity of 1 for each fragment Note however that any charge or spin multiplicity settings in the atomic section must be compatible with any settings for overall charge and spin specified by the Jaguar 6 0 User Manual 147 Chapter 7 Using Jaguar 148 molchg and multip keywords in the gen section For more information about the atomic section see Section 9 8 on page 226 After saving the input file with the atomic section you can run it in Jaguar in the usual manner You do not need to set iguess because Jaguar will choose the most appropriate guess for the system under study If you have an antiferromag
42. generating input with new geometry 149 in solution sese 73 186 194 initial Hessian for ssss 40 41 89 90 171 189 234 235 input file section for Hessian 234 235 key wotds eere sense 186 191 limiting step size for 190 191 194 maximum number of iterations 89 149 187 Jaguar 6 0 User Manual 351 Index 352 output description eene 118 output of forces 117 output options 137 refinement of initial Hessian for 40 41 97 98 171 172 189 Di I ees aeons 149 troubleshooting eee 295 trust radius for 190 191 194 updating of Hessian during 189 see also transition state optimization geometry SCANS eeeenennnennesnnenennnnnnnnnnnnennennnn 98 102 Geometry Symmetrizer dialog box 45 geometry translation and rotation of during calculation otiose geopt program ghost atoms use in charge fitting to bond T dpoints 4 neenon ege 125 Gibbs free energy calculations 83 84 130 200 gradient see analytic gradient of energy Cirasp prOgrAm con ceccecieiepe ret oret reina 197 grid and RwR information keyword for OUtpUt OE acerca sen auteur 213 grid file default ion area eitis 243 description and format 254 256 specifying in input file
43. key WOId ieee erneuten ttes 175 Maestro setting essen 42 molecular properties See properties molecular state keywords 175 molecular structure see geometry input geometry optimization Molecule folder 54 Moller Plesset second order perturbation theory see LMP2 Monitor panel 27 31 49 mouse functions neeeeeeenenennnennnnennennennnnnnnnnnenennnen 3 Project Table panel 16 17 WOEkSpaCe uitae Hiper rrr 10 MP2 see LMP nennen 178 MPI flags setting een 306 mpi ch Utility aniei 301 MOM basis set file bas keyword 215 Mulliken population analysis 76 for basis functions ueeseesesesennenenennen 76 Ia 197 output from uuesennennenennennnenenennn 128 129 output of multipole moments from 129 recalculating multipole moments from 76 Mulliken spin populations 76 multiple Jaguar jobs running from Maestro see 49 51 with jaguar batch 282 286 multiplicity key Wofil 175 setting in Maestro sss 42 43 multipole moments calculan aoi sesiis 76 150 from electrostatic potential fitting 75 76 125 from Mulliken population analysis 76 129 keyword a eden reme 196 output description 124 output opti Oi se erii ir 137 tensors listed in output 124 units keyword
44. one using B3LYP 6 311 G and the other using LMP2 6 311 G The batch file for this process given below would read in each molecular geometry from an existing input file make the necessary keyword changes and perform the calculations B3LYP 6 31G geometry optimization SJOB SJOB_dft_opt igeopt 1 basis 6 31g dftname b3lyp remove igeopt setting for the following single point calculations and change basis set to 6 311 G OPTIONS igeopt NONE basis 6 311 g run B3LYP single point calculation SJOB_dft_opt 01 SJOB_dft_sp change level of theory to LMP2 and run single point calculation SJOB_dft_opt 01 JOB lmp2 sp dftname NONE mp2 3 Jaguar 6 0 User Manual 287 Chapter 11 Running Jobs 288 11 3 3 2 Running Jobs from Input in a Specified Directory The script below runs jobs for a set of input files in a specified directory using two different sets of options and places the output in subdirectories of the launch directory Define protocol 1 OPTIONS basis midi dftname x3lyp icfit 1 Create the job directory and cd into it All job files will be written to this directory if WORKDIR and OUTDIR are set to the same directory name WORKDIR protocolli OUTDIR protocoll Get the input files append protol to each add the OPTIONS keywords and run them through Jaguar SJOB JOB protol Now go back to the original launch directory create the directory for protocol2 and repeat the cal
45. restart file to cc pWTZ f and restart the job See Section 7 5 on page 150 for a description of how to restart jobs This procedure will generally be significantly faster than running a GVB LMP2 cc pVTZ f job from scratch Jaguar 6 0 User Manual 67 Chapter 4 Options 68 Jaguar jaguar Silex Use structures from Workspace included entries 1 Molecule Theory scr Properties Solvation Output Accuracy level Quick zd m Convergence criteria Maximum iterations 48 Energy change 5e 05 hartree RMS density matrix change 5e 06 Convergence methods SCF level shift 0 00 hartree Thermal smearing None 10000 00 A Convergence scheme Dis za Force convergence use with caution see iacscf keyword in the manual Orhitals Fixed symmetry populations Final localization None zi Job GVB LMP2 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 4 5 The SCF folder 4 8 SCF Settings The SCF folder includes various settings that control the type of calculation and how the calcu lation is performed including the accuracy level the convergence method and criteria and the orbital symmetry and localization 4 8 1 Accuracy Level Jaguar can use integrals evaluated on a grid with the pseudospectral method and fully analytic integrals The grids used for various SCF iterations and the
46. secure servers MPICH uees 300 Select Batch Script panel 51 selection states see object types for selection self consistent reaction field method for solvation calcul tiotis corn reet shells information in output shortcut keys main window Project Table panel Simons method for trust radius adjustment key WOE assessment eine 190 singlet open shell keyword for 207 SOoleptOgrani eterne ener 240 Output MOM hen 123 SOLVPIOSTaM ae 240 output from sse 121 SOlvatiOD one iei erede ita 71 73 enere y Output nn alten 123 keywords for 194 195 output from calculations 120 124 probe radius cte 72 195 Solvent Chol66 1 acere cete T3 van der Waals radii 120 229 260 268 Solvation folder siseses 72 solvent parameters csse 13 SPARTAN archive files 139 215 spin density surface 84 222 spin multiplicity keyWord iisimmin 175 setting in Maestro 42 43 spin populations Mulliken 76 SQM frequency scaling method 80 81 ssh use with MPICH 300 standard functionals dftname values for 180 standard output key Words ee eee ette 212 213 Maestro options unenenenenennennenn 135 138 Start dialog box 47 269 structure input s
47. the results are incorporated into the project according to the settings used to launch the job If a job that is not currently being monitored ends you can select it in the Monitor panel and click Monitor to incorporate the results Monitored jobs are incorporated only if they are part of the current project You can monitor jobs that are not part of the current project but their results are not incorporated To add their results to a project you must open the project and import the results Jaguar 6 0 User Manual 27 Chapter 2 Introduction to Maestro 28 2 11 Getting Help Maestro comes with automatic context sensitive help Auto Help Balloon Help tooltips an online help facility and a user manual To get help follow the steps below Check the Auto Help text box at the bottom of the main window If help is available for the task you are performing it is automatically displayed there It describes what actions are needed to perform the task If your question concerns a GUI element such as a button or option there may be Bal loon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Help menu of the main window If there is Balloon Help for the element it appears within a few seconds If you do not find the help you need using either of the steps above click the Help button in the lower right corner of the appropriate panel T
48. v 6Z d 8S8LI LL SO OL W SLIM VvL eL LJH CL I LG H 95 sI SS IEI cel 9ET OFI IVT HYL SPI vel SCIL STI SCIL LUL OCT vel SPI COT I61 91T ax PSII eslar zejas IS S OS UI 6r PO 8t 9V Lp Pd Op UN srina PIAL erlow CP QN Irl z OP A GE IS B8E Ta LE TUL PUL OFT OCT col OCT SCE LUE STI OFT LUL LUL SUL col TET vr T VLL EOT IM O9t d St 9 vt SV t 9D CCED IE UZ 0EIND 6c IN 86 00 LTA 9c UIN SCHO YTA ETIL CC S ITED OTA 61 860 660 TOT 90T ITE SIT 9 I VSL IV 8I ID LI S 9I d SI IS TI IV l sw CI EN II IL O TLO ELO SLO LDO T80 060 CI N Old 60O 8N LID 9 S ed pI 60 TEO PH 7 H I 8 amp G uonaas ui pequosep se ejy ndul ue JO UOIJ26S JJwoje ay ui sBuies Aoo Buryew Aq paJej e eq ueo suas snipel eseu z Jo anjen JIneJap e YIM pJOM Oy SI 26JAOO 8J8UM IPLI JUBJCAOD JI JO WINS BY saw 298JAO9 ULY SS J SI WAY uaeMjeq eauejsip eui J pepuoq suloje OM sJepisuoo senber Kje1auay swiojy uaamjag spuog se yong uoinogioju Jo sjoAe ajenjeA3 oj pesf suiousDuy ul pey Jusjer09 GP 6 algeL Jaguar 6 0 User Manual 232 Chapter 9 The Jaguar Input File Three other keywords shown in Table 9 46 allow you to specify whether to include grid points dealiasing functions or nuclear charges for listed atoms The values n no none and only are not case sensitive You can use the atomic section to specify counterpois
49. 0 7 trans 2 methylcyclopropanoic 4 6 5 0 0 4 butanoic 4 5 4 8 0 3 cis 2 chlorobut 2 enoic 3 5 2 8 0 7 trans 2 chlorobut 2 enoic 3 3 3 2 0 1 cis 3 chlorobut 2 enoic 3 9 4 1 0 2 trans 3 chlorobut 2 enoic 3 5 3 9 0 4 2 chlorobut 3 enoic 2 9 2 6 0 3 cis 4 chlorobut 3 enoic 4 3 4 1 0 2 trans 4 chlorobut 3 enoic 4 2 4 1 0 1 3 oxobutanoic 5 0 3 6 1 4 benzoic 3 9 4 2 0 3 trans cinnamic 4 4 4 4 0 0 2 furanecarboxylic 3 5 3 2 0 3 malic 3 0 3 4 0 4 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation THIOLS methylthiol 9 7 10 3 0 6 ethylthiol 10 3 10 6 0 3 2 mercaptoethanol 9 2 9 4 0 2 2 propylthiol 10 8 10 9 0 1 2 oxopropylthiol 8 5 7 9 0 6 t butylthiol 11 7 11 2 0 5 SULFONAMIDES N chlorotolylsulfonamide 4 4 4 5 0 1 dichlorphenamide 7 3 7 4 0 1 mafenide 9 1 8 5 0 6 methanesulfonamide 10 0 10 5 0 5 quinethazone 9 1 9 3 0 2 saccharin 2 8 1 3 1 5 sulfamethizole 4 0 5 4 1 4 sulfaperin 6 7 6 8 0 1 sulfacetamide 5 9 5 4 0 5 sulfadiazine 6 1 6 5 0 4 sulfadimethoxine 6 7 6 0 0 7 sulfamethazine 7 0 7 4 0 4 sulfanylamide 10 8 10 4 0 4 sulfapyridine 7 5 8 4 0 9 sulfaquinoxaline 5 8 5 5 0 3 sulthiame 11 0 10 0 1 0 nimesulide 6 0 3 9 0 1 xipamide 9 0 10 0 1 0 Jaguar 6 0 User Manual 319 Chapter 14 The pK Prediction Module 320 Table 14 2 Molecules used in the pK parametrizati
50. 0 Calculate energy but do not update wave function do only one iteration gt 0 Perform a maximum of maxit SCF iterations default value is 48 newcon 0 Use physical constants and conversion factors equivalent to those used in GAUSSIAN 86 1 Use physical constants and conversion factors equivalent to those used in GAUSSIAN 88 90 92 iacc 1 Only ultrafine grid used tight cutoffs 2 Accurate mixed grid types accurate cutoffs default choice for transition metals sometimes for other atoms beyond Ar 3 Quick mixed grid types looser cutoffs Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description iacscf 0 Make no special adjustments variable vshift cutoff adjustments etc for convergence 1 Start with level shift vshift of 5 0 and decrement over 10 iterations to 0 8 keep number of canonical orbitals fixed during optimization run at ultrafine accuracy level and with tight cutoffs 2 Start with level shift vshift of 6 0 and decrement over 12 iterations to 0 8 vary level shift during run by raising it when SCF is restarted here when the energy rises by 0 0001 au 3 Use extreme cutoffs maximal analytic corrections while still allowing medium pseudospectral grids for some iterations 4 Same as iacscf 1 except with maximal analytic corrections jksep 0 2J K formed for core when
51. 1 16 0 1612778 1 0000000 0 1813806 H1 5 L lt 0 2 17 1 1000000 1 0000000 1 6057611 H2 1 3 0 1 20 18 7311370 0 0334946 0 2149354 H2 2 1 0 1 20 2 8253944 0 2347270 0 3645712 H2 3 1 0 1 20 0 6401217 0 8137573 0 4150514 H2 4 1 0 1 21 0 1612778 1 0000000 0 1813806 H2 5 T 4 2 22 1 1000000 1 0000000 1 6057611 The second table an example of which follows below shows information for the Cartesian components of each shell For instance the entries X Y and Z for the tenth shell correspond to Px p and p functions The normalization for each Cartesian component depends on the powers of x y and z in the polynomial for the component For 2 and higher the normaliza tion can be different for different components The rmfac values provide the ratio of the normalization to that of the first component listed which is the x component Jaguar 6 0 User Manual 133 Chapter 6 Output Gaussian Functions Normalized coefficients S h t e y l p f atom 1 e n Zz rcoef rmfac rcoef rmfac Oo 1 S 1 5484 671660 0 831724 1 000000 0 831724 Oo 2 S 1 825 234946 1 530816 1 000000 1 530816 Oo 3 S 1 188 046958 2 477149 1 000000 2 477149 Oo 4 S 1 52 964500 3 256281 1 000000 3 256281 Oo 5 Ss 1 16 897570 2 792893 1 000000 2 792893 Oo 6 S 1 5 799635 0 954938 1 000000 0 954938 Oo 7 38 2 15 539616 0 617934 1 000000 0 617934 Oo 8 S 2 3 599934 0 275721 1 000000 0 275721 Oo 9 S 2 1 013762 0 814208 1 000000 0 814208 Oo 10 x 3 15 539616 3 116
52. 120 number of iterations has not been exceeded the output notes molecular structure not yet converged and the optimization continues The output next lists the movement of the center of mass If the output option for the bond length and angles is enabled the output then lists this information for the new structure Finally the nuclear repulsion energy for the new geometry is listed If the molecular structure was not yet converged and the maximum number of geometry opti mization iterations allowed was not reached in the previous iteration the output from more geometry optimization iterations follow The output from each iteration begins with onee grid and rwr output in the usual formats and continues with output from sc which now starts with the calculation type and the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output further continues with output in the usual formats from der1a rwr and der1b winding up with the output from geopt The last such geometry optimization iteration contains in the geopt output either the line Geometry optimization complete or the line stopping optimization maximum number of iterations reached depending on whether the convergence criteria were met before the maximum number of iterations was reached 6 3 5 Solvation Performing a solvation calculation involves several iterations in which the wave functions for
53. 13 in the gen section depending on which orbitals are printed Relevant orbital output keyword set to 4 9 or 14 in the gen section depending on which orbitals are printed Relevant orbital output keyword set to 5 10 or 15 in the gen section depending on which orbitals are printed Relevant orbital output keyword set to 6 11 or 16 in the gen section depending on which orbitals are printed Jaguar 6 0 User Manual Chapter 6 Output Fortran formats The word labels indicates that the atom identifiers for instance h2 and the basis function types for instance S for s Z for p or XX for d are shown Note that in canonical orbital space the labels indicating atom identifiers and basis function types are meaningless The output for each style is shown in either table form or list form When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital 1s listed in turn with the basis function coefficients listed in order For the third and fourth options those with f19 15 and f8 5 formatting all coefficients are listed in order but without numbering The three styles presented in list form also include information on the occupation and energy of each orbital If you generate output in the f19 15 or f8 5 formats you can use it for input in the guess section of an input file
54. 135 140 209 217 OUtPUL oM 1e trrti tren rte 135 Build panel ioco ten 19 building structures eee 18 21 button MEDU u a 7 C canonical orbital space output in 216 Cartesian coordinates format for geometry 36 37 170 freezing for geometry optimization 37 91 92 CH DEOBEAITE itin en rete ipte OT ORENSE SERE 240 output from 120 121 123 129 charge fitting see ESP fitting Mulliken population analysis charge molecular key WOFdS a cose cts iscsi encsis attin ne 175 setting in Maestro sessies 42 charges atomic from ESP fit o noie eee 74 keyword for formal 228 Mulliken tere deett ere 76 chemical shifts sss 77 199 CIS calculations 63 185 CLS prOgTam iioii tete en initiis 240 command options jaguar run 276 Command Script Editor panel 24 command scripts see scripts comment lines Datoh SCHIP tics ER 282 input file m dtes 167 170 configuration interaction CI CI singles calculations 63 185 energy lowering for GVB pair natural Orbitals 4aecidvecetesciieeine ite 117 connectivity keyword for bonding 174 Jaguar 6 0 User Manual output keyword oo eee eee 213 output option oes etii eireas 137 constraints HAITI 92 173 equivalent coordinates
55. 187 SCE eiecerunt 69 148 202 J J2 theory calculations sess 52 jagconvert utility 2er 281 jaguar command 272 281 including in PATH 290 jaguar babel 278 281 jaguar batch 282 286 jaguar Rhelp u coeen treten 273 jaguar TODE 213 Jaguar lll 278 jaguar machid nesessrauenene 273 jaguar platform 273 jaguar results 105 110 Jaguar Fun eiecti 275 277 Jaguar SyS EG a 273 Jaguar copyright information 110 Jaguar data directory sss 243 Jaguar files nii eee 243 Jaguar panel unse ae 33 Jaguar programs seen 239 Jaguar Read dialog box sss 42 Jaguar Write dialog box sess 46 jexeoc prOBram eie isti ee tetra 239 job directory local sss 48 52 job nare eee 48 110 272 277 jobs running in Maestro 26 27 K keywords atomic mass eeeeeeeeneenennennnennnnnnnnnnnn 175 176 dealiasing function 218 file output nn 214 frequency related properties 199 geometry optimization eee 186 CTI acces E 218 GVB ionem teen ieri 176 Initial guess iiec 206 lewis dot structure 176 localization memory usage orbital output Propertie Srann iii Jaguar 6 0 User Manual SCF iteratie iorsin cientes 215 solvation cesses eene 194 standard output
56. 24 on page 195 causes the virial ratio V T to be printed out at the end of each SCF calculation Table 9 32 Output keywords and their settings Keyword Value Description ipl 2 Gaussian function list for basis set ip3 2 Gaussian function list for dealiasing functions ip4 2 Number of dealiasing functions used ip5 2 Memory disk and i o information Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 32 Output keywords and their settings Continued Keyword Value Description ip6 2 Timing information user CPU and user system CPU 2 Timing information user cpu and wall clock ip7 2 Grid shell locations ip8 2 Gaussian function list for derivatives of basis functions ip11 2 Bond lengths and angles 3 Same as setting ip11 2 but includes all internuclear distances regardless of connectivity and torsions 4 Same as setting ip11 3 but includes all possible angles regardless of atom connectivity 5 Same as setting ip11 4 but includes all possible torsions regardless of atom connectivity ip12 2 Connectivity table ip13 2 Eigenvectors and eigenvalues of overlap matrix ip18 2 Overlap matrix ip19 2 One electron Hamiltonian ip20 2 Additional output from RwR including inverse condition numbers and dealiasing functions associated with small eigenvalues of RwR ip23 2 Additional DFT grid information ip24 2 All keyword settings including internal ones ip25 2 Multipole moments in atomic units and Debye ip26 2 Geo
57. 4 Options 80 Jaguar jaguar EN mix Use structures from Workspace included entries 1 Molecule Theory scr Properties Solvation Output Properties select to edit options Calculate Property vibrational frequencies Surfaces MO density potential E Atomic electrostatic potential charges ESP Mulliken populations EUR San N80 analysis Multipole moments Polarizability Hyperpolarizability Vibrational frequencies MEAM Use available Hessian Thermochemistry 4 IR Intensities Pressure 1 00 atm Atomic masses Most abundant isotopes Start temperature 298 15 K j Ere e Scaling Increment 10 00 K None Number of steps 4 v Pulay SQM method B3LYP 6 31G factors Output units v Scaling factor kcal mol w kJ mol 0 7500 Start Read Write Edit Reset Close Help Figure 4 9 The Properties folder showing controls for vibrational frequencies 4 11 3 Scaling of Frequencies Because the errors in quantum mechanical calculations of frequencies are often fairly predict able it is sometimes desirable to scale frequencies by one or more factors Scaling methods can also improve calculations of thermochemical properties which use the scaled frequencies In Jaguar two options are available for frequency scaling the Pulay et al Modified Scaled Quantum Mechanical Forc
58. 7 0 4 ethylamine 11 1 10 7 0 4 1 propylamine 10 5 10 7 0 2 t butylamine 10 9 10 7 0 2 2 aminoethanol 8 8 9 5 0 7 2 aminoacetamide 8 7 7 9 0 8 2 aminoacetonitrile 53 53 0 0 2 amino 2 methylpropane 1 3 diol 8 7 8 8 0 1 3 aminopropanol 9 3 10 0 0 7 SECONDARY AMINES dimethylamine 10 8 10 7 0 1 diethylamine 10 8 11 0 0 2 azetidine 11 0 11 3 0 3 aziridine 71 8 0 0 9 pyrrolidine 10 9 11 3 0 4 Jaguar 6 0 User Manual 321 Chapter 14 The pK Prediction Module 322 Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation piperidine 10 8 11 1 0 3 morpholine 9 4 8 5 0 9 2 hydroxyethyl ethylamine 10 1 10 0 0 1 bis 2 hydroxyethyl amine 9 0 8 9 0 1 N methylamino acetamide 9 0 8 9 0 1 TERTIARY AMINES trimethylamine 10 1 9 8 0 3 triethylamine 10 5 10 8 0 3 tripropylamine 9 6 10 7 1 1 1 methylpiperidine 10 4 10 2 0 2 triallylamine 8 0 8 3 0 3 1 allylpiperidine 10 0 9 6 0 4 dimethylcyclohexylamine 10 5 10 7 0 2 dimethylbenzylamine 9 3 9 0 0 3 diethylbenzylamine 9 6 9 4 0 2 N methylaziridine 8 5 7 9 0 6 N methylpyrrolidine 10 5 10 4 0 1 bis 2 hydroxyethyl methylamine 8 4 8 5 0 1 ANILINES aniline 4 6 4 6 0 0 2 chloroaniline 2 8 2 4 0 1 3 chloroaniline 3 6 3 5 0 1 4 chloroaniline 4 0 4 0 0 0 2 methoxyaniline 4 7 4 5 0 2 3 methoxyaniline 4 2 4 2 0 0 4 methoxyaniline 5 4 5 4 0 0 3 nitroaniline 2 2 25 0 3 Jaguar 6 0 User Manual Chapter 14 The pK Pre
59. As described in Section 7 4 on page 150 you must specify lone pairs for either all or none of the lone pairs on any particular atom Change the lone pair information and try running the calculation again Jaguar 6 0 User Manual Chapter 12 Troubleshooting The SCF calculation does not converge properly or frequencies or other properties look wrong If the geometry entered is of poor quality the calculation may not converge prop erly which may also lead to inaccurate calculation of molecular properties If you are performing a geometry optimization check to see whether the geometry changes are rea sonable if you are performing a single point calculation make sure the structure entered is appropriate You might want to minimize the structure with a molecular mechanics program first If the structure is reasonable convergence problems should not occur and we would appreciate it if you would describe them to us at the address given on page 334 preferably by e mailing us the input output and log files for the job with a brief explana tion To get converged results in the meantime you can try using level shifting and or set ting the accuracy level to Ultrafine both of which are described in Section 4 8 3 on page 70 and Section 4 8 1 on page 68 The calculation will be slower but convergence may be better for problem cases The settings available in the Start dialog box are not what you expected them to be Many of the options are
60. Chem 1982 3 385 Rabuck A D Scuseria G E J Chem Phys 1999 110 695 Bayly C L Cieplak P Cornell W D Kollman P A J Phys Chem 1993 97 10269 Stroud A H Approximate Calculation of Multiple Integrals Prentice Hall New York 1971 Lebedev V I Zh vychisl Mat mat Fiz 1975 15 48 54 Lebedev V I Zh vychisl Mat mat Fiz 1976 16 293 306 Lebedev V I Sibirsk Mat Zh 1977 18 132 142 Lebedev V I In Theory of Cubature Formula and Numerical Mathematics in Russian Sobolev S L Ed Nauka Sibirsk Otdel Novosibirsk 1980 pp 110 114 Cramer C J Truhlar D G J Comp Aided Mol Design 1992 6 629 Marten B Kim K Cortis C Friesner R A Murphy R B Ringnalda M N Sitkoff D Honig B New Model for Calculation of Solvation Free Energies Correc tion of Self Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects J Phys Chem 1996 100 11775 Chasman D Beachy M D Wang L Friesner R A Parallel Pseudospectral Elec tronic Structure I Hartree Fock Calculations J Comput Chem 1998 9 1017 Beachy M D Chasman D Murphy R B Friesner R A Parallel Pseudospectral Electronic Structure II Localized Mgller Plesset Calculations J Comput Chem 1998 19 1030 Jang Y H Sowers L C Cagin T Goddard W A III J Phys Chem A 2001 105 274 Jaguar 6 0 User Manual Reference
61. Input File se 167 9 17 input FIE Formal a een 167 9 1 2 Sections Describing the Molecule and Calculation 168 9 2 The zmat zmat2 and zmat3 Sections esses 170 9 3 The zvar zvar2 and zvar3 Sections uu0uuneennssnnennnnnnnennennnnnnnnnn 171 9 4 The coord and connect Sections sess 172 9 5 rhe GEN Sectlol agent denti teet tetefi efte tens 9 5 1 Geometry Input Keywords 9 5 2 Molecular State Keywords Charge and Multiplicity s 175 9 5 3 Atomic Mass Keyword toile ot toii e deese Di estes EL HERI eL Re Eo EAHRLdSSc da 175 9 5 4 Symmetry Related KeywoLtls tetas teca taste estu pde de o dee pda niaaa 176 9 5 5 GVB and Lewis Dot Structure Keywords eeeeeen 176 9 5 6 MP2 Key WOIGS i iiir ci ert PH I PRO PH NEIN IS FH PINO MEI FEET ERN 178 9 5 7 DPI Key WOFOS sarei nr ER eI Evae Fa E E A 179 9 5 8 GIS REV WORKS 5 ET 185 9 5 9 Geometry Optimization and Transition State Keywords 186 9 5 10 Geometry Scan Key WOrdS caisccsssssssessisassastcsansieaacasdcrcetesteaccaaseesceasoniaasesacvaecna 192 9 5 11 Intrinsic Reaction Coordinate IRC Keywords sees 192 9 5 12 Solvation Keywords nennen 194 Jaguar 6 0 User Manual Contents 9 5 13 Properties Keywords na 196 9 5 14 Fr
62. Jaguar however For more details on NBO input and output see the NBO 5 0 Manual or visit the NBO web site http www chem wisc edu nbo5 4 10 5 Polarizability and Hyperpolarizability You can calculate polarizabilities and first and second hyperpolarizabilities by selecting Polar izability Hyperpolarizability in the Properties table and making the appropriate choice from the Property Method option menu The calculations can be done analytically or with a finite field The analytic method calculates the polarizability and hyperpolarizabilities by solving the coupled perturbed Hartree Fock CPHF equations In general this method is superior to the finite field method but the CPHF option can be used only with closed shell and unrestricted open shell wave functions The options for the finite field method 17 can use a 3 point 5 point or 7 point finite difference method which uses the results from a number of SCF calculations one with no field and several with electric fields that are multiples of E and E in the x y and z directions E is 0 024 au by default You can use a different value by entering it in the Finite field text box Both hyperpolarizability methods are run without using molecular symmetry Also for any polarizability calculation the energy convergence criterion which is set in the SCF folder is set by default to 1 0x10 For more information see Section 6 3 7 on page 124 and Section 9 5 13 on p
63. Kr Cd H Ar 101 Xe Hg Bi LAV3P K H Ar Cu Rb Ag Cs La Hf Au LACVP ERMLER2 K Lr H Ar 6 31G o H Ar 102 109 Ga Kr In Xe TI Rn The Cundari Stevens ECP basis set 101 named CSDZ has been provided to cover the lanthanides This basis set uses a relativistic effective core potential for the inner core electrons and treats the outer core and valence electrons with a 4s 4p 2d 2f basis set The ECP basis set developed by Ermler and coworkers 102 107 named ERMLER2 is also available The basis set provided is the small core set that includes the outer core orbitals in the valence space in the same way as the LACV basis sets The basis set is a double zeta contraction in which the outermost primitive function in each symmetry has been uncon tracted The core is treated by a relativistic effective core potential for all elements For TI Rn the refitted ECPs have been taken from Wildman et al 108 but the basis set from the original ECPs has been retained because the new basis sets are much larger and do not match the basis sets for the other elements Polarization and diffuse functions for the 4p 5p and 6p elements have been added from the relativistic all electron double zeta set of Dyall 109 Jaguar 6 0 User Manual Chapter 4 Options In Table 4 2 the atoms described by the effective core potential are listed first followed by the atoms described by the alternate basis set or sets The
64. Nuclear mass in amu esp Electrostatic potential fitted point charge or request to fit charge to dummy atom see text formal Formal charge integer value on atom multip Spin multiplicity of atom or fragment containing atom 2spin Number of unpaired alpha or beta electrons on atom positive value for alpha spin negative value for beta spin mulk Mulliken population vdw van der Waals radii in for charge fitting vdw2 van der Waals radii in for solvation cov Covalent radius in used to determine bonding and other properties The formal keyword is useful for solvation jobs because the van der Waals radii are adjusted according to the chemical structure found by Jaguar and for generating an improved initial guess for transition metal containing systems along with the multip keyword See Section 7 1 3 on page 147 for more information on using this improved initial guess method The esp keyword can be used to freeze the charge on an atom to a particular value while fitting charges to other atoms leave an atom out of charge fitting or fit a charge to a dummy atom If the esp column entry for an atom is set to a real number the atomic charge for that atom will be held fixed to that number during charge fitting If the esp column entry for an atom is set to n or no or 0 the atom will not be included in charge fitting If the esp column entry for a 6 dummy atom is y or yes it will be included in the
65. Related Keywords By default for most calculations Jaguar takes advantage molecular symmetry to reduce computing time as described in Section 3 7 2 on page 44 Several integer valued keywords shown in Table 9 5 describe how the program uses symmetry Table 9 5 Symmetry related keywords in Jaguar Keyword Value Description isymm 0 Do not use symmetry 1 Rotate atomic grids to match molecular symmetry if possible 2 Change grids to get molecular symmetry if necessary 8 Use symmetry in preprocessing and SCF ipopsym 0 Allow change in number of electrons in each irreducible representa tion default for HF and DFT closed shell jobs 1 Don t allow number of electrons in each irreducible representation to change default for non HF non DFT and open shell calculations idoabe 0 Allow non Abelian point group symmetry assignment 1 Allow only Abelian point group symmetry assignment 9 5 5 GVB and Lewis Dot Structure Keywords The ihfgvb keyword allows you to specify the initial guess to be used for a generalized valence bond GVB calculation By default ihfgvb is set to 0 The ihfgvb keyword is described in Section 9 5 17 on page 206 GVB pairs are set in the gvb section and a GVB calculation will be performed any time one or more GVB pairs are described in the input file This includes the use of the igvball keyword You can find Lewis dot structures by setting the appropriate keywords and you can also use one of these structures
66. SCAN PESSE einen 192 scanhess 22220000202200000000nnneennnnennennennene 192 SCONV 195 SOlvent a2 na 195 SUITS nee 201 204 T MPINI seen tmpstp tradmn cnl engeren piro q M treok ioo ud eei etie trescal uoce nei incur ces M juil EE V VOW 228 WOW 2 i cstsinetenidiiitet Uo eras Aa e atis 228 vshift 184 202 202 202 203 204 Ww WISDG ote e eet ee uror datas tetas 196 198 X cnp 223 xcorl1 xcorl4 184 185 Jaguar 6 0 User Manual 363 Keyword Index 364 yexll eene iet etes 184 VERDI dendo ete iet ise 184 yexnli yexnl9 ueneseenenenn 184 jS M M 184 ymaxadj 4 o eeenioeliemese diete 223 yminadJ 22 0 223 Jaguar 6 0 User Manual 120 West 45th Street 1500 SW First Avenue 3655 Nobel Drive Dynamostrafe 13 32nd Floor Suite 1180 Suite 430 68165 Mannheim New York NY 10036 Portland OR 97201 San Diego CA 92122 Germany SCHR DINGER
67. Si A 0 i k o amp amp 4 Rotate around Y axis by 90 degrees Rotate the Workspace contents around the Y axis by 90 degrees Reset Workspace Reset the rotation translation and zoom of the Workspace to the default state Restore view Restore the last saved view of the Work space orientation location and zoom Display only Choose a predefined atom category Open the Atom Selection dialog box Undisplay Choose a predefined atom category Open the Atom Selection dialog box Show hide or color ribbons Choose to show or hide ribbons Choose a color scheme for coloring rib bons Draw atoms in CPK Choose an object type for drawing bonds in CPK representation Open the Atom Selection dialog box Click to select atoms for representation Double click to apply to all atoms Draw bonds in tube Choose an object type for drawing bonds in tube representation Open the Atom Selection dialog box Click to select atoms for representation Double click to apply to all atoms Color residue by constant color Choose a color for applying to residues Click to select residues to color Double click to color all atoms Label picked atoms Choose an object type for labeling atoms Open the Atom Selection dialog box Open the Atom Labels panel at the Com position folder Delete labels Click to select atoms to label Double click to l
68. The default localization procedure is Pipek Mezey 50 localization but you can choose Boys 49 local ization or an alternate Pipek Mezey localization see Section 9 5 6 on page 178 These schemes are available from the Valence localization method option menu In LMP2 unlike in canonical MP2 the correlating virtual space for each occupied orbital is limited to those orbitals that are localized on the atoms of the local occupied Hartree Fock orbital The localization of the occupied orbitals makes this limitation of the virtual space a good approximation and leads to a reduction in the basis set superposition error In the limit that all local virtual orbitals are assigned to every occupied orbital the local MP2 method and the canonical MP2 method are exactly equivalent All calculation types available for LMP2 wave functions are also available with the local local MP2 method which allows you to treat only some atoms at the LMP2 level while the remaining atoms are treated at the HF level Local local MP2 calculations use orbitals that are localized on the specified atom pairs After the localization of the canonical Hartree Fock orbitals the atomic orbital coefficients for each localized orbital are summed for each atom and the orbital is considered localized on the two atoms whose coefficient sums are largest If the largest coefficient sum on one atom is more than ten times as large as the coefficient sum on any other atom the locali
69. W SLIM PLIL LJH CL I LG ed 9 9D ss TOTT 0scc SETT OCT 961 c TETT ver T PLOT OSPI v9 TL ISP TL 16671 90 TL 88 TL COCT 97 TL ICT LO ax PSII eslar zejas sjus OSU 6v PO 8t 9V Lp Pd Op UN Sb hW vb amp XL erjow CP QN IZ or a 6 S selau LE ILOT S60 C COLT SITT OPET TOLT ISET BLT LIT 9er T 987p T OST TIS T CELO T Z88 T LOT OOL T 9061 IM O9t d St 9S vt sSV ECOD Ct D IE UZ Ot nOD 6C IN 8c 0D LTA 9c UIN SCHO VC tC lL TEOS ITED OTA 6l veel PLOT 0061 PLOT LVU C 6vcC OIS I I6F I IV 8I ID LIS 9I d SI ISS TI IV El SIN CL EN II Ic9 I T89 T 009 T 009 T 006 T HOT ELEI OTTI N Olja 60O 8N LO 94 ed pI ISTI 0Sr T 9H 7 H I C6 192I suogejnojeo uonenjos 10 sjueuiuBisse snipes sjeey Jep ueA uo UOREUIOJUI 910W 104 ejy ejep siwe nejep eui pue 9 0 uoioes 6 uogoes eeg sdnojB jeuorounj ureji8o ui suioje 10 Ipea sjsn pe Ayeiaueb senber eouis soey pjoq ui umous 31e MoJaq senje amp A snipes asoym SWOJE 10 peuDisseae eq ULI Ipes suomejnojeo uoneAJos 104 swonsbuy ul IIpeH SIEBM Jap UBA rr 6 aiqel 231 Jaguar 6 0 User Manual The Jaguar Input File Chapter 9 9VI LVI SV I 6VI vel OCT LUIT OCT 8CI OCT vel PHT 691 861 SET 1g 8 dd c8 LL I8 9H O8
70. accuracy with which parts of the calculation are done greatly affect the timing and sometimes the accuracy of the entire calcu Jaguar 6 0 User Manual Chapter 4 Options lation You can adjust the grids and the set of cutoff values determining these factors using the Accuracy level option menu For more information on grids and cutoffs see Section 10 4 on page 254 and Section 10 5 on page 257 The default Quick setting allows fast calculations to be performed using several different pseudospectral grid types and cutoffs that should generally produce well converged energies The Accurate setting which corresponds to tighter cutoffs and therefore somewhat slower calculations also uses a variety of pseudospectral grids If you choose the Ultrafine setting the cutoffs are even tighter very accurate and only the ultrafine pseudospectral grid type is used The Ultrafine setting may be helpful for cases with convergence or accuracy problems but increases the computational cost by a factor of two to three The final choice is Fully analytic which turns off the pseudospectral method and uses the analytic methods for all integrals 111 112 This choice is significantly slower than the pseu dospectral method 4 8 2 Convergence Criteria SCF calculations finish when the calculations converge the maximum number of iterations is exceeded or Jaguar determines that the calculation cannot converge The maximum number of iterations
71. additional files For each of the options described below the relevant file appears in the same directory as the output file Each file name is in the form jobname suffix where the different suffixes for each kind of file are described below If you make a setting in the Output folder the output from the program pre lists the non default options chosen This output appears above the molecular geometry output from pre and gives the non default values of the keywords referred to in footnotes in this section Gaussian input file gau When this option is selected a file in the format of a GAUSSIAN input file is created with the suffix gau The file information includes the molecular geometry the basis set name and 9 Keyword ip18 2 in the gen section 10 Keyword ip19 2 in the gen section 11 Keyword ip1 2 in the gen section 12 Keyword ip8 2 in the gen section 13 Keyword ip160 2 in the gen section Jaguar 6 0 User Manual Chapter 6 Output the type of calculation to be performed as well as the molecular charge and the spin multi plicity of the molecule and any relevant effective core potential information If symmetry is turned off that setting will be entered into the gau file For GVB calculations you should specify GVB pairs Jaguar will also generate a GVB initial guess which will be included in the gau file For more information on setting up GAUSSIAN input files see Section 7 6 on page 151 GA
72. and the convergence criteria are set in the Convergence criteria section You can set the maximum number of SCF iterations in the Maximum iterations text box Generally Hartree Fock calculations for simple organic molecules converge in fewer than 10 iterations while complex calculations using higher level methods or involving open shells can take a few extra iterations Molecules that include transition metals can converge more slowly The default energy convergence criterion which can be set in the Energy change text box is 5 0x10 Hartrees When the change in total energy on consecutive iterations is less than this value the energy is converged For polarizability calculations the default is 1 0x10 Hartrees If the energy difference is less than 1 of the previous energy difference however this conver gence criterion is overridden for that iteration and the calculation continues The default density convergence criterion which can be set in the RMS density matrix change text box is 5 0x10 When the RMS difference in density matrix elements between two iterations is less than this value the density is converged For polarizability and hyperpo larizability calculations if the energy convergence criterion described in the previous para 42 Keyword iace 3 in the gen section 43 Keyword iace 2 in the gen section 44 Keyword iace in the gen section 45 Keyword nops 1 in the gen section 46 Keyword maxit in the gen se
73. are also some unique command options for the jaguar batch command which are summarized in Table 11 8 Table 11 8 The jaguar batch command line options Option Description c Create input files but don t run the batch job f Restart option Skip execution of steps that are completed i e steps that have input files and completed output files The default action is to generate Jaguar input files from template files even if they overwrite previously existing files and run the corresponding job step 1 Lists jobs that would be run if jaguar batch were called without options but does not generate any files or run any jobs s Lists jobs that would be run and shows the contents of the input files that would be gen erated if jaguar batch were called without options but does not generate any files or run any jobs The r option is a restart option which prevents jaguar batch from overwriting existing Jaguar input and output files and from running the job steps that created them The 1 and s options permit you to see what jaguar batch would do but do not actually allow it to generate any new input files or run any Jaguar jobs The jaguar batch command accepts both Jaguar input files jobname in and Maestro files jobname mae as input and you can specify both on the same command line Maestro files are used as a source of structures only and jaguar batch creates a Jaguar input file for each structure in the Maestro file using
74. atoms are not in the correct order you must edit the geometries to place them in the correct order For best results the reactant and product structures should not be radically different from the transition state For instance to find the transition state in a bond breaking reaction it would be better to provide a product structure in which the breaking bond was fairly long and weak than a true minimum energy structure in which the bond had completely dissociated Jaguar 6 0 User Manual 95 Chapter 5 Optimizations and Scans 96 The reactant and product structures are added to the zmat2 and zmat3 sections of the input file for QST searches and to the zmat and zmat2 sections for LST searches If you want to edit the structures you can do so in the Edit Job dialog box When you select Structure in this dialog box the three structures are available in separate folders labeled Reactant Product and Tran sition State If you want to use the same Z matrix for all geometries choose Standardize Z matrix format from the Structures menu You can then set any variables to the desired values If you want to apply constraints in the search you must add them to the main geometry The main geometry for the job is the topmost in the Structures section the transition state for stan dard and QST searches and the reactant for LST searches To add constraints click the inclu sion button for the main geometry then add the constraints in th
75. be specified using the p option or the MPI_P4SSPORT environment variable otherwise the standard port number 1234 is used Table 13 1 Commands for the mpich script Command Action start Start servers stop Kill servers restart Kill and restart servers status Report server status Jaguar 6 0 User Manual 301 Chapter 13 Parallel Jaguar 302 Table 13 1 Commands for the mpich script Command Action pid Report server PID sems Report semaphore sets in use rmsems Delete all semaphore sets shm Report shared memory segments in use rmshm Delete shared memory segments see text below rmipcs Delete both semaphores and shared memory segments config Describe the MPICH configuration Table 13 2 Options for the mpich script Option Meaning p port Specify the port number for servers The default port is 1234 m hostfile Specify a file listing the MPICH host machines The default file is machines LINUX h host list Act just on the specified hosts The default is to act on all hosts specified in the host file u user Connect to remote machines as the specified user v Report the version number of the mpi ch script d Provide debugging output The secure server can also be launched manually on each machine with the command usr lib mpich bin serv p4 o p port You can also launch the secure servers within a job by setting the environment variable SCHRODINGER MPI START in the shell in which the jo
76. be useful for obtaining an estimate of basis set superposition error BSSE For LMP2 calculations see Section 4 5 on page 63 the LMP2 correction is already designed to avoid basis set superposition error so we advise computing only the Hartree Fock counterpoise correction term To specify a counterpoise atom place an sign after the atom s label For example to place sodium basis functions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in an input file Nal 0 0 0 0 1 0 3 4 8 Specifying Coordinates for Hessian Refinement If you are optimizing a molecular structure to obtain a transition state you might want to refine the Hessian used for the job Section 5 3 on page 93 explains the methods used for transition state optimizations including Hessian refinement This subsection explains only how to edit your input to specify particular coordinates for Hessian refinement Whether or not you refine particular coordinates you can specify a certain number of the lowest eigenvectors of the Hessian for refinement as described in Section 5 3 4 on page 97 the Hessian can be refined in both ways in the same job Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro If you type an asterisk after a coordinate value Jaguar computes the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightly and uses the re
77. bonded metals must be assigned to separate fragments All atoms must be assigned because all unassigned atoms are assumed to be in the same fragment Finally add formal and 2spin values in the atomic section 9 9 The hess Section If an input file has a non empty hess section the keyword inhess in the gen section is set to 2 automatically and a Hessian is read in from the hess section Since for a Hessian H Hj Hi only the elements with j i are read in and the program symmetrizes the matrix itself later Since the Hessian has dimensions of 3Nx3N where N is the number of atoms including dummy atoms it may be large so files listing all elements in each row by order of rows could be unwieldy and difficult for the user to read Therefore the Hessian is assumed to be presented in blocks composed of five columns each with the last block possibly having fewer than five columns if 3N is not a multiple of five The format used for the hess section is the same as that used in GAUSSIAN files or BIOGRAF hes files All Hessian elements for dummy atoms should be set to 0 as they are in Jaguar output Each set of elements from a block of five columns should be preceded by a line containing one or more arbitrary integer labels for instance column labels could be convenient for keeping track of the elements when looking at the hess section All of the elements within a five column block for which j the column indicator is less than or equal
78. can be stored in the Project Table as properties of the mole cule To do so click Create Properties For any entry that has these properties set you can set the charge and spin multiplicity for the calculation by selecting Use charge and multiplicity from Project Table 3 7 Cleaning up Molecular Geometries The molecular geometry sometimes needs improvement before you perform calculations For example it might not have the desired molecular symmetry or it might be far from the minimum or transition state Maestro has options to clean up the geometry for calculations in both of these cases The options are available from the Build panel which you can open by clicking the Open Close Build panel toolbar button in the main window F The changes made in this window are not applied until you click OK To check the effect on the geometry you must close the window and open the Edit Geometry or Edit Input window If you want to be able to restore the previous geometry after inspecting the new geometry save the geometry using the Save dialog box before opening the Geometry Cleanup window 3 7 1 Quick Geometry Optimization You can clean up the geometry by clicking the Geometry Cleanup toolbar button in the Build panel Maestro first performs a quick charge equilibration Qeq calculation to obtain partial charges for all atoms in the system and then uses those charges in an energy minimization based on Goddard and Rappe s Universal Force F
79. case there is no need to select an eigenvector or to set the itrvec keyword If you do not wish to use the QST method then you should check the output file from your transition state search job while it is running to ensure that the desired mode was selected For each negative Hessian eigenvalue Jaguar prints out the internal coordinates that dominate the corresponding eigenvector If you find that the wrong mode is being followed kill the job and select the desired eigenvector index either in the GUI or by setting itrvec in the gen section of the input file The order and the character of the eigenvectors can change during an optimization To ensure that the optimization follows the eigenvector that most closely correlates with the one chosen in the previous iteration select Follow same eigenvector Otherwise the optimization follows the eigenvector of the same index number as the previous iteration 5 3 4 Refinement of the Initial Hessian The quality of the Hessian in the initial steps of a transition state optimization can have a marked effect on the speed of the job since the Hessian controls the direction the optimization takes on a potential energy surface in the search for an appropriate saddle point The QST guided transition search method effectively refines the Hessian automatically in the first steps along the circular curve connecting the reactant transition state guess and product With the standard non QST guided opti
80. charge fit Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Several warnings apply to the use of the esp column First the esp settings must not be incon sistent with the symmetry used for the rest of the job Second you should be careful not to overconstrain the charge fitting job Third if you are including any dummy atoms in the charge fitting it may be advisable to perform the charge fitting in a separate job based on the restart file for which the charge fitting grid has been altered to include points around the dummy atoms by including a grid column in the atomic section with y or yes entries for the dummy atoms as described below The van der Waals surface used for charge fitting is constructed using DREIDING 60 van der Waals radii for hydrogen and for carbon through argon and universal force field 57 van der Waals radii for all other elements These radii are listed in Table 9 43 and can be changed using the vdw keyword The van der Waals radii for solvation calculations are listed in Table 9 44 and can be changed using the vdw2 keyword The radii for the elements H C N O F P Cl Br and I can be adjusted by Jaguar in some functional groups See Section 10 6 on page 260 for more informa tion on how Jaguar uses these radii in solvation calculations The covalent radii used to determine which atoms are bonded are given in Table 9 45 Two atoms are considered to be bonded if the distance bet
81. convenient 1 J and K for core are kept separate maxdiis 10 Number of Fock matrices to use in DIIS extrapolation noatcor 0 Analytic corrections calculated 1 No analytic corrections calculated nops 0 Use pseudospectral method to calculate J and K operators 1 Construct J and K from analytic four center two electron integrals no grid used noupdat 0 Fock matrix updating 132 set on or off automatically 1 No Fock matrix updating set iacc 1 if you set noupdat 1 iteravg 0 Do not average density matrices and adjust orbitals accordingly unless istavg keyword requests averaging gt 0 For iterations whose number is n iteravg 1 where n is an integer revise orbitals so that they correspond to average of density matrices from pre ceding and current iterations istavg 0 Do not average density matrices and adjust orbitals accordingly unless iteravg keyword requests averaging gt 0 For iterations whose number is lt istavg revise orbitals so that they corre spond to average of density matrices from preceding and current iterations noauto 0 Grid choice is automatic 1 All calculations done on coarse grid Jaguar 6 0 User Manual 203 Chapter 9 The Jaguar Input File Table 9 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description 2 All calculations done on medium grid 3 All calculations done on fine grid 4 All calculations done on ultrafine grid idenavg 0 Converge in
82. determined by the schrodinger hosts file used for the job This file is the schrodinger hosts file found in the directory from which Maestro was started if it exists otherwise it is the schrodinger hosts file in your home directory if that file exists and if neither of those two files exists the default schrodinger hosts file for the submission host is used If you are using a different schrodinger hosts file from what you expect or if you are working with a new version of Jaguar and a new schrodinger hosts file has been installed on your computer you should examine the schrodinger hosts file for the job and make sure it is in the correct form and that the settings are appropriate See Section 11 1 on page 269 for a description of the schrodinger hosts file The job fails with a memory related error Memory fault out of memory or no memory available for array for example or the log file indicates Killed for the job Your job may have failed because the machine was too heavily loaded in which case rerunning the job when the load is lower could solve the problem Otherwise you might want to try an appropriate setting from Section 9 5 25 on page 219 to avoid a problem for a large job or you and or your system manager might want to investigate increasing the maximum virtual size or the soft limit allowed for memory on your machine Contact us as described on page 334 if you would like any tips for setting memor
83. distance between the two hydrogen atoms is 1 507 angstroms amp zmat o hi o 0 95 h2 o 0 95 hi 105 amp Now suppose you want to optimize the geometry subject to the constraint that the distance between the hydrogen atoms is 2 0 Then you would add the following coord section amp coord hi h2 2 0 amp You can also specify a variable after the sign separated by a space The values that the vari able takes must be given in a zvar section The following example defines a variable HH as the distance between H1 and H2 amp coord H1 H2 HH amp Jaguar 6 0 User Manual 173 Chapter 9 The Jaguar Input File 174 You can use a connect section to specify the bonds used by Jaguar in its generation of internal coordinates Each line of a connect section should list two atoms by either their atom labels such as H2 for a hydrogen or their atom numbers such as 3 for the third atom listed in the zmat section input Here is a sample connect section amp connect C1 C2 C2 C3 amp The two atoms on each line of the connect section are then treated as nearest neighbors by the program when it generates redundant internal coordinates for the optimization Consequently the internal coordinates generated by Jaguar include the bond between those two atoms and angles between those two atoms and any other atoms that are nearest neighbors to either of them For the sample connect section above for instance the redu
84. diverse set of molecules including those containing polyfunctional groups and conformational flexibility to evaluate the robustness of the method ology For the molecules considered below it appears to be quite satisfactory For example for protonation of nitrogens in heterocycles an average prediction accuracy of 0 19 is obtained over 16 molecules whose pK values range from 0 65 to 9 17 Our empirical corrections take the simple linear form pK a pK raw b a That is we assume that the correction terms obey a linear free energy relationship The b term is similar to our previously employed surface tension corrections for solvation of neutral species The linear term takes into account the significant variation in charge on the ionizable Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module group as a function of substituents Consider for example carboxylic acids The charge on the oxygens in the CO moiety varies by as much as 0 45 eu when electron withdrawing substitu ents such as in oxalic acid are replaced by electron donating substituents such as in propi onic acid This change in charge alters the hydrogen bonding first shell correction term as well as the solvation free energy computed by the SCRF calculation Since changes in the raw pK are well correlated with these charge shifts linearly scaling the correction term to the raw pK is capable of capturing this effect While corrections to the solvat
85. due to elimination of basis set superposition error 48 However localized MP2 implementations in conventional electronic structure codes have not yet led to substantial reductions in CPU time since the first few steps of the necessary four index trans formation are unaffected by localization of the occupied orbitals and the localized orbitals have tails that extend throughout the molecule Jaguar 6 0 User Manual 161 Chapter 8 Theory 162 We have carried out extensive tests demonstrating the accuracy and computational efficiency of the pseudospectral implementation of LMP2 as detailed in ref 16 In the pseudospectral approach we assemble two electron integrals over molecular orbitals directly and are thus able to fully profit from the huge reduction in the size of the virtual space in Pulay s theory Formally the PS implementation of LMP2 scales as nN however various types of cutoffs and multigrid procedures can reduce this to N In fact for calculations involving both the 6 31G and Dunning cc pVTZ basis sets we find a scaling N with system size The physical idea behind the LMP2 method is that if the molecular orbitals are transformed so that they are localized on bonds or electron pairs correlation among the occupied pairs can be described by the local orbital pairs and their respective local pair virtual spaces defined from the atomic orbitals on the relevant atom or pair of atoms The localized orbitals can be g
86. each atom s bonds and hybridization type The element and chemical environment of each atom determine its atom type When Jaguar reads the Lewis file it sets the atom s van der Waals radius to the value dictated by the first atom type description in the Lewis file that matches that atom For instance if the atom were a methyl carbon and the first atom type description in the file was of a carbon bound to a hydrogen the radius would be set to the radius matching that description even if a later line in the Lewis file described a carbon bound to three hydrogens Atom types are determined by an atom s element and by any combination of the following other properties Hybridization for example sp Bonding type which is determined by the bond orders of the bond s the atom forms and the element s to which the atom is bonded Hybridization type which describes the hybridization and element of atoms to which the original atom is bonded e Ring size the size of the ring the atom is in for instance 6 for a carbon in benzene Aromaticity of the ring the atom is in if any An aromatic ring is defined here by the Huckel Rule if the ring contains 4n 2 pi electrons where n is any non negative integer it is considered to be aromatic The Lewis file first determines the bonding types and hybridization types that will be recog nized then lists atomic radii for various atom types The file contains different versions of this informat
87. files created by Jaguar are written is determined by the setting in the Directory folder of the Preferences panel The default local job directory is the directory from which you read the input file if you read one or the directory you were in when you started Maestro See Section 2 8 on page 25 for more information 3 9 2 Job Submission Options In the Job section you can provide a job name select the execution host the number of processors and the scratch directory The choices available in the Job section depend on the schrodinger hosts configuration file See Section 11 1 on page 269 for more information on this file The job name can be entered in the Name text box If the structure you are using for input is a named entry in the Project Table the entry name appears in the Name text box The names of the input output and log files for your job depend on the name you provide the Jaguar input file is named jobname in the output file is named jobname out and the log file is named Jobname log For instance if the job name is h2o the results are stored in a file called h2o out within the local job directory If the structure is a scratch entry a default name is selected The execution host the machine that the job will run on can be selected from the Host option menu This menu lists all the hosts available in the schrodinger hosts file The default execution host is localhost which means the machine on which Maestro is running
88. fine ultrafine eldens for electron density calculations and gradient By default Jaguar uses the coarse grid for electron density calculations and the ultrafine grid for gradient Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files calculations and the extreme grid is included for testing purposes so the number of grid types in the file default grid is actually five Jaguar uses the grids upon each atom in the molecule provided by the grid file to generate molecular grids All grids for each basis set are then listed in turn The basis set is identified with a BASIS line and containing its name and is followed by a blank line Each molecular grid description starts with two comment lines usually a blank line followed by a descriptive line The next line contains an integer flag which determines which points from the atomic grids for the atoms in a molecule are included in the molecular grid Jaguar generates a boundary plane between the two atoms and perpendicular to the vector between them disposing of any points from one atom that are on the other atom s side of the boundary plane The integer flag determines the location of this plane if the flag is 0 the plane is located so that the ratio of the distances of the atoms to the plane is the same as the ratio of their cova lent radii while if it is 1 the boundary plane is set where the grid point density from each atom on the vector between the atoms is equal The grid p
89. first set of buttons opens various panels that allow you to perform functions on the entries in the Project Table The second set of buttons controls the ePlayer which plays through the selected struc tures each structure is displayed in the Workspace in sequence at a given time interval See Section 2 3 2 on page 7 for a description of the types of toolbar buttons The buttons are described below Find Open the Find panel for locating alphanumeric text in any column of the Project Table except for the row number Sort Open the Sort panel for sorting entries by up to three properties NI lt Plot Open the Plot panel for plotting entry properties r 7 E BE s Import Structure Open the Import panel for importing structures into the project Export Structure Open the Export panel for exporting structures to a file Columns Choose an option for adjusting the column widths Select only Open the Entry Selection dialog box for selecting entries based on criteria for entry proper ties Jaguar 6 0 User Manual 13 Chapter 2 Introduction to Maestro 14 Go to start I4 4 Display the first selected structure Previous E Display the previous structure in the list of selected structures Play backward 4 Display the selected structures in sequence moving toward the first Stop E Stop the ePlayer Play forward b Display the selected structures in sequence moving toward the last Next
90. five hybridization groups for that atom Each group must begin with the word Group with no leading spaces The group is a list of bonded atoms for all relevant hybridization types of those bonded atoms for instance Group 2 for hydrogen could describe hydrogens Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files bonded to sp carbons by listing carbon s atomic number under an sp hybridization label Because there is no default number of hybridizations described for each group unlike for the bonding type information where each group contained sets for three bond orders the first line under each group label must begin with the number of hybridizations described for that group after any number of spaces The next line dictates a hybridization for the bonded elements about to be described Hybrid ization labels must start with five spaces followed by one of the following character strings s hybridization p hybridization d hybridization sp hybridization sp2 hybridization Sp3 hybridization sp3d hybridization sp3d2 hybridization For each hybridization the bonded elements with that hybridization are then listed in two lines the first indicating the number of elements and the second indicating the elements themselves as for the bonding type information Information for any following atoms should be preceded by a line with three asterisks and a blank line indicates the end of the hybridization type information
91. folder that is displayed in a panel click the Help but ton in the panel The Help panel is opened and a relevant help topic is displayed For other information in the online help open the Help panel and locate the topic by searching or by category You can open the Help panel by choosing Help from the Help menu on the main menu bar or by pressing CTRL H To view a list of all available Jaguar related help topics click the Categories tab then from the Categories menu choose Jaguar Double click a topic title to view the topic If you do not find the information you need in the Maestro help system check the following Sources Maestro User Manual for detailed information on using Maestro Maestro Command Reference Manual for information on Maestro commands Jaguar Quick Start Guide for a tutorial introduction to Jaguar The NBO 5 0 Manual for information about NBO calculations Frequently Asked Questions pages located at http www schrodinger com Support fags html Jaguar 6 0 Quick Start Guide 333 Chapter 15 Getting Help 334 The manuals are also available in PDF format from the documentation page of the Schr dinger web site at http www schrodinger com Support pdf html Information on additions and corrections to the manuals is available from this web page If you have questions that are not answered from any of the above sources contact Schr dinger using the information below E mail help schrodinger
92. from Maestro the log file is written to the local job directory The log file notes when each section of Jaguar is complete as well as noting data from each iteration in an SCF calculation as it is calculated You can view this file in the Monitor panel which is displayed when a job is launched or when you choose Monitor from the Applications menu in the main window See Section 6 7 on page 142 for more information on this file The primary Jaguar output is contained in the output file which is created in the scratch direc tory of the host on which the calculation is run and is copied back to the local host when the job finishes The output file is described in Chapter 6 3 12 J2 Theory Calculations If you want to calculate energies accurately you can perform J2 theory calculations 25 using a predefined batch script The J2 batch script performs a B3LYP 6 31G geometry optimiza tion and frequency calculation followed by single point GVB LMP2 calculations using the cc pvtz f and cc pvtz basis sets at the B3LYP optimized geometries These single point calculations are used to determine a basis set correction energy A parameterized electron pair correction energy is also added The final J2 energy is an absolute enthalpy at 298K The finite temperature effects are calculated from the B3LYP frequencies The J2 results do not include a standard heat of formation because the relevant calculations for the constituent atoms are not made
93. from Schr dinger run with geldens 3 and denspcz 0 3 or smaller for best results denspc 0 75 Spacing in bohrs of rectangular grid for electron density calculation mulken 0 Do not calculate Mulliken populations 1 Calculate Mulliken populations by atom 2 Calculate Mulliken populations by basis function and by atom 3 Calculate Mulliken bond populations nmr 0 Do not calculate NMR shielding constants 1 Calculate NMR shielding constants Analytic polarizabilities amp and hyperpolarizabilities B and y are available for HF UHF DFT and UDFT methods The definition of B changed with Jaguar 5 5 and differs by a factor of 0 5 from that used in previous versions of Jaguar The new definition is now consistent with that used in GAUSSIAN The definitions of polarizabilities ot first hyperpolarizabilities B and second hyperpolarizabilities y are Jaguar 6 0 User Manual 197 Chapter 9 The Jaguar Input File 198 2 3 4 NE E TET _dE EF k qEdEdKE WM GF dF dF dF If you want to calculate polarizabilities with the old definition you must set iopt332 332 in the gen section and you can only calculate o and for closed shell wave functions The finite field methods corresponding to ipolar gt 0 differ in the data they use for numerical differentiation The 3 point method uses the results from seven SCF calculations one with no field one with a field of E whose input is described below in the x direction one wi
94. geometry optimization iteration see Section 5 1 1 on page 88 for more information and examining the output summary of the Hessian eigenvectors which indicates the dominant internal coordinates and their coefficients for each eigenvector 20 Keyword itrvec 0 in the gen section 21 Keyword itrvec 1 in the gen section 22 Keyword itrvec 2 in the gen section 23 Keyword itrvec gt 0 in the gen section 24 Keyword itrvec 5 in the gen section 25 Keyword itrvec gt 0 in the gen section where itrvec is the relevant eigenvector number for the selected eigen vector Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans You can also determine the eigenvector to follow from a vibrational frequency calculation However because different mass weighting schemes are used in vibrational frequency calcula tions and transition state searches it is possible for the two calculations to produce a different number of negative Hessian eigenvalues for a non stationary point If you select the mode to follow based on the results of a vibrational frequency calculation you might discover that the mode actually followed is different and that the number of negative Hessian eigenvalues has changed There are two ways around this problem The preferred way is to use the QST guided algorithm which automatically selects the mode that best connects the reactant and product geometries with the transition state guess geometry In this
95. has a Scratch directory listing of scr for a job called n2o Jaguar attempts to create the directory scr erwin h2o and write files there during the job If your job gives error messages related to the temporary directory you should check to make sure that the temporary directory listed in the Start dialog box exists and that you have write permission within that directory For example if the output Error creating or cd ing to temp directory scr erwin h2o appeared in the h20 1og file for erwin s job it could be because scr erwin did not exist or because erwin did not have permission to make the subdirectory h2o within it If you are running parallel or distributed jobs you might not have permission to create a directory on one of the hosts Jaguar 6 0 User Manual Chapter 12 Troubleshooting You might need someone to create the appropriate temporary directory or change permissions on it from the root account Use the command 1s 1 to get information on ownership of your temporary directory or the directory above it If you need to be able to create a subdirectory within a directory owned by root or another account that does not belong to you and for which you do not have write permission contact your system administrator for help 12 1 5 Problems Running Jaguar Calculations on Other Nodes In order to launch jobs on other nodes and for these nodes to copy files back to the host from which they were submitted the nodes must be ab
96. incorporated To display the surfaces create an entry in the Project Table for the chosen molecule and select it then choose Import from the Surfaces submenu of the Display menu The Import Surface Volume Data diaolg box is displayed and you can navigate to the vis files for the surfaces and import them Then choose Surface Table from the Surfaces submenu of the Display menu to open the Surface Table panel 91 Keyword tmpstp in the gen section 92 Keyword ntemp in the gen section 93 Keyword ip28 2 in the gen section 94 Keyword iplotesp 1 in the gen section 95 Keyword iplotden 1 in the gen section 96 Keyword iplotspn 1 in the gen section 97 Keywords iorbla iorb2a iorb1b iorb2b in the gen section 98 Keywords xadj yadj zadj in the gen section 99 Keyword plotres 1 in the gen section Jaguar 6 0 User Manual Chapter 4 Options Jaguar jaguar xj ev x Use structures from Workspace included entries 1 Molecule Theory scr Properties Solvation Output Properties select to edit options Calculate Property vibrational frequencies _ as Surfaces MO density potential Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability Surface s MMMM Electrostatic potential Box size adjustment 0 00 side Electron density Grid density s oo pts 4 Spin den
97. interpreted as a single command In this document to type text means to type the required text in the specified location and to enter text means to type the required text then press the ENTER key References to literature sources are given in square brackets like this 10 Jaguar 6 0 User Manual xiii Document Conventions xiv Jaguar 6 0 User Manual Chapter 1 Introduction The Jaguar User Manual is intended to help you perform ab initio calculations for a variety of methods parameters and calculated properties Jaguar can be run from the command line or from the Maestro graphical user interface GUI Online help is available in the GUI although the information in this manual is generally more comprehensive Chapter 2 introduces the main features of Maestro and provides instructions for setting up your environment and running Maestro Chapter 3 contains information you will need to run Jaguar including information about using the GUI geometry input formats specifying file names for input and output displaying molec ular geometries symmetrizing geometries and setting run time parameters such as the machine that will perform the calculation We suggest you start by trying the sample calcula tion in Section 3 1 If the calculation runs successfully you can proceed to the rest of the chapter to learn how to input molecular structures and run jobs If you have problems starting Maestro or running the sample calc
98. is 0 1 tradmn 0 01 Minimum trust radius allowed during optimization for itradj gt 0 see trust information tremx 0 25 Trust radius reduction criterion if relative error between actual and pre dicted energy changes is more than tremx and itradj gt 0 trust radius is reduced trgmx 0 0 Trust radius reduction criterion for itradj gt 0 and trgmx gt 0 if absolute error in a component of predicted gradient exceeds trgmx hartrees bohr trust radius is reduced Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 20 Keywords for trust radius adjustment Continued Keyword Value Description treok 0 2 Criterion for increasing trust radius if itradj 2 and relative error between actual and predicted energy changes is less than treok trust radius is increased treok default is 0 2 trescal 2 0 Scale factor for trust radius adjustment used only when itradj 2 The keywords shown in Table 9 21 may be used to specify the geometry convergence criteria or these criteria may be scaled to five times their default values with the keyword setting iaccg 3 for a quicker coarser calculation The first four keywords listed in Table 9 21 have units of hartrees bohr gconv5 and gconv6 have units of bohrs and gconv7 has units of hartrees SCF calculations performed for each new structure generated during an optimization are judged to be converged when they meet the criterion for the root mean square of the change in dens
99. is 1 2 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 2 Options for the keyword iunit Keyword Value Description iunit 0 Geometry units are bohr and radians 1 Geometry units are angstroms and degrees 2 Geometry units are bohr and degrees 3 Geometry units are angstroms and radians 9 5 2 Molecular State Keywords Charge and Multiplicity The keywords that describe the input molecule s charge and spin multiplicity are shown in Table 9 3 These keywords correspond to GUI options described in Section 3 6 on page 42 Table 9 3 Keywords to describe the molecular state Keyword Value Description molchg any Overall charge on molecule excluding point charges set in pointch section default is 0 multip 20 Spin multiplicity 1 for singlet 2 for doublet etc default is 1 except for ihamtyp 0 when multip 2 by default 9 5 3 Atomic Mass Keyword The keyword massav determines the atomic masses used for any atoms whose masses or isotopes are not specifically set in the atomic section see Section 9 8 on page 226 The masses used are from ref 124 Table 9 4 Keyword to describe the atomic masses used Keyword Value Description massav 0 Use masses of most abundant isotopes as atomic masses 1 Use average isotopic masses as atomic masses where averages are weighted according to natural abundance of isotopes Jaguar 6 0 User Manual 175 Chapter 9 The Jaguar Input File 176 9 5 4 Symmetry
100. is entered in the hess section whether directly or from a restart file for a calculation that performed a Hessian evaluation and symmetry is on the IRC calculation might not produce any points or might not produce points on the actual reaction path if the transition state has higher symmetry than the reaction path If this is the case you should turn symmetry off isymm 0 in the gen section If you evaluate the Hessian with inhess 4 in the gen section symmetry is turned off for analytic Hessian calculations and the subsequent IRC calculations are done without symmetry The IRC calculation can fail if the step size is too small The warning message states that the vector used to determine the step is too small You can increase the step size by setting ircstep in the gen section The IRC calculation can also fail if the potential energy surface is very flat and the gradient that is used to find the next IRC point is too small You can change the cutoff for determining when the gradient is too small with the keyword ircgcut If you set this keyword you should be careful not to set it so small that it does not filter out noise in the gradient The restart file for an IRC job includes the geometry of the last found IRC point This geom etry is in the zmat section An iremode downhill setting is included in the gen section regard less of the initial setting as a restart job proceeds downhill from the last found IRC point If the job has not pr
101. it is no larger than the trust radius the maximum element of nuclear displacement and the root mean square element of the nuclear displacement The predicted energy change for the new structure generated by geopt is also listed The values for the energy change gradient and nuclear displacement described in the previous paragraph are important because they are each tested against the convergence criteria deter mined by the Convergence criteria setting in the Optimization folder as described in Section 5 1 on page 87 or alternatively the criteria set by the gconv keywords in the input file The criteria are described in detail in Section 9 5 9 on page 186 If the gradients are converged and the energy change is below 2 5 x 107 the optimization stops unless it is on the first geom etry optimization iteration Similarly if the gradients are converged and one of the gradient criteria is 5 times lower than the convergence level then the optimization stops if the energy change is less than 2 5 x 10 The symbol following each quantity used to judge convergence indicates how well converged it is The symbol indicates convergence criteria that are not satisfied indicates criteria that are satisfied indicates criteria that are quite well satisfied essentially zero If the convergence criteria mentioned are not met and if the maximum so indicates values that are Jaguar 6 0 User Manual 119 Chapter 6 Output
102. job Do not incorporate do not add the output structures and properties from the job to the project The results are available in the output directory including the output file the Jag uar restart file and a Maestro structure file This is the only available option if you run the job with a scratch entry or choose Selected structure files as the source of structural input The choice that you make from this menu is persistent the next time you run a Jaguar job the incorporation mode that you last used is the default mode The incorporation mode is stored as a preference by Maestro so the choice persists across Maestro sessions Jaguar 6 0 User Manual 47 Chapter 3 Running Jaguar From Maestro 48 The results of this job will not be incorporated because the Workspace contains a Scratch entry Would you like to make this entry a real entry run with a Scratch entry or cancel Create Entry Run With Scratch Cancel Figure 3 7 Scratch entry alert box If your job input is a scratch entry an alert box Figure 3 7 is displayed when you click Start before the Start dialog box is displayed This box prompts you to create a named entry from the scratch entry If you then click Run With Scratch Do not incorporate is automatically selected in the Start dialog box and the Incorporate controls are unavailable The job can be run but it cannot be incorporated into the project The local directory where input and output
103. keywords cierre better 213 Index local MP2 method see LMP2 method local LMP2 method locat program eene 240 localization of orbitals GVB LMP2 calculations 67 keywords 179 208 LMP2 calculations 64 179 options for final sess 71 log file iecit 142 143 batch JObSza ien nt tercer 51 in Monitor panel eee 49 saving Maestro seen 28 M MACHA Program 240 machines LINUX file 299 301 macros see scripts Maestro interface behavior sees 3 main window sese 4 5 lun 6 Monitor panel sess 31 49 problems starting sess 291 292 quit llg EEE E tete 28 running jobs from eese 26 27 Scratch Projects nee 11 Starting ena ae d d none D 4 undoing operations s s s 26 main window esee 3 makejbasis utility sss 247 masses for frequency calculations 79 keyword setting in atomic section memory keywords 219 220 troubleshooting related to 295 memory disk and i o information keyword nennen 212 output option 135 136 Men button enero rre ra eae 7 minimum energy path MEP calculations 102 Molden orbitals file mol keyword for 215 molecular charge
104. kl Display the next structure in the list of selected structures Go to end b kl Display the last selected structure Loop Choose an option for repeating the display of the structures Single Direction displays struc 4 tures ina single direction then repeats Oscillate reverses direction each time the beginning or end of the list is reached The status display to the right of the toolbar buttons shows the number of selected entries When you pause the cursor over the status display the Balloon Help shows the total number of entries the number shown in the table the number selected and the number included in the Workspace 2 4 2 The Project Table Menus Table find text sort entries plot properties import and export structures and configure the Project Table e Select select all entries none invert your selection or select classes of entries using the Entry Selection dialog box and the Filter panel Entry include or exclude entries from the Workspace display or hide entries in the Project Table and perform various operations on the selected entries Property display and manipulate entry properties in the Project Table ePlayer view entries in succession stop reverse and set the ePlayer options Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro 2 4 3 Selecting Entries Many operations in Maestro are performed on the entries selected in the Project Table The Project Table func
105. on the main menu bar or with the Display Connect amp Fuse panel on the Build toolbar IX Replace one or more atoms in the existing fragment with another fragment by selecting a fragment and clicking in the Workspace on the main atom to be replaced Grow another fragment by selecting Grow in the Build panel and clicking the fragment you want to add in the Fragments folder Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Build build Emi Atom Residue Properties Properties Fragment Place 7 Grow Define grow bond F Pick Atoms Fragments Organic zi Grow Direction forward a Joining Geometry anti Close Help Figure 2 4 The Build panel Grow mode uses predefined rules to connect a fragment to the grow bond The grow bond is marked by a green arrow The new fragment replaces the atom at the head of the arrow on the grow bond and all atoms attached to it To change the grow bond choose Bonds from the Pick option menu in the Build panel and click on the desired grow bond in the Workspace The arrow points to the atom nearest to where you clicked To draw a structure freehand 1 Choose an element from the Draw button menu on the Build panel toolbar F 2 Click in the Workspace to place an atom of that element 3 Click again to place another atom and connect it to the previous atom 4 Continue this process until you have drawn the structure 5 Click the
106. or atom label of the atom associated with the lone pair and the same atom number or label repeated once more Either all or none of the lone pairs on an atom should be specified as GVB lone pairs and these GVB lone pairs should be identified by consecutive numbers starting with 101 Thus if the molecule had one lone pair on atom 2 and two on atom 5 the lines describing them would contain the numbers 101 2 2 101 5 5 and 102 5 5 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Three more entries may be added onto the ends of all of the lines specifying the pairs these entries are present in new input files generated during or after calculations The first value should be set to 0 The next two values if they exist give the CI coefficients for the first and second GVB natural orbitals in each pair The first coefficient should always be positive and its magnitude should always be greater than that of the second coefficient which should always be negative These coefficients are included in new input files so that if you restart the calculation with the new input file the contributions of each GVB natural orbital are known The sample gvb section that follows sets a sigma bond pair between atom 1 and atom 2 and two lone pairs on atom 1 amp gvb i 12 10111 10211 amp 9 7 The Imp2 Section The Imp2 section whose GUI equivalent is described in Section 4 5 on page 63 is not keyword based The section
107. or density difference matrix if Fock matrix updating was done ip121 All J and K matrices in atomic orbital space ip122 Fock matrix in atomic orbital space HF or molecular orbital space GVB ip123 Fock matrix in canonical orbital space ip149 GVB data f a b etc ip188 Debug printing for automatic cutoff convergence scheme ip201 Total electronic density integrated on the DFT grid a See text in this subsection for information on ip152 The keyword ipvirt determines how many of the virtual orbitals are printed in the output file and in the restart new input file Virtual orbitals are printed in order of increasing energy The virtual orbitals are obtained by diagonalizing A gt f 2J K where f is the fractional occupation of each orbital 1 for a closed shell If ipvirt 1 all virtual orbitals are printed in the output and restart files otherwise ipvirt virtual orbitals are printed if that many virtual orbitals exist By default ipvirt 10 Several possible formats and levels of information can be requested for each other keyword determining the orbitals printed The choice of keywords which are listed in Table 9 35 deter mines the stage or stages at which orbitals are printed the keyword values determine which orbitals are printed and the format of the printing These settings can generally also be made from the GUI as described in Section 6 6 on page 139 Table 9 35 Keywords that specify when to print orbitals
108. other table entries provide the same information as that given in the previous table except that the polarization functions are only applied to atoms obtained from the non ECP basis sets with the exception of the ERMLER2 basis sets All ECP basis sets use five d functions as described earlier in this section Currently the LACVP LAV3P and LACV3P basis sets use the pseudospectral method while all other ECP basis sets use the analytic method We strongly recommend using either the LACVP or the LACV3P basis set for non lanthanide molecules containing atoms beyond Ar in the periodic table especially for studies involving charge transfer d metals or correlated wave functions The LACV3P basis set seems to give substantial improvements over the LACVP basis set for HF LDA and B3LYP atomic state splittings The LACV3P basis set which includes a diffuse d function on any metal atoms is useful for calculations on anions or low spin M 0 complexes of the late first row metals 4 3 Density Functional Theory DFT Settings The density functional theory module in Jaguar allows you to employ a variety of functionals to describe exchange and correlation for either open or closed shell systems The theory is described in Section 8 4 on page 164 This section describes how to set up a DFT calculation in Jaguar You can perform DFT geometry optimizations solvation calculations charge fitting and all other calculations and properties available for Hart
109. page 56 and Table 4 2 on page 58 to obtain this basis set information Because the available basis sets are not designed for core correlation you should not use the mp2 1 setting Calculations performed with this setting are likely to be misleading and can have large pseudospectral error Local MP2 calculations use the LMP2 method for all atoms unless the Imp2 section described in Section 9 7 on page 225 is used to set local LMP2 pairs or unless the keyword iheter is set to 1 The iheter and mp2 keyword settings are described in Table 9 7 For LMP2 calculations Jaguar needs to obtain localized orbitals By default Jaguar uses the Pipek Mezey method to perform the localization If Pipek Mezey localization does not converge for a particular case you might want to try Boys localization by changing the settings for the keywords loclmp2c and loclmp2v as indicated in Table 9 7 If you are performing a set of calculations to compare against each other you should use the same localization method for all of the calculations Table 9 7 Keyword settings for local MP2 calculations Keyword Value Description mp2 0 Do not run LMP2 calculation 1 Correlate core and valence electrons not recommended see text 3 Run LMP2 calculation for valence electrons only iheter 0 Treat all atoms with LMP2 if LMP2 is on unless Imp2 section exists if LMP2 is on and Imp2 section exists set atom pairs in Imp2 section 1 Treat only heteroatom pairs atoms in bon
110. performed from the Project Table panel For more information see Section 2 4 on page 11 Edit undo actions build and modify structures define command scripts and macros and find atoms in the Workspace Display control the display of the contents of the Workspace arrange panels and dis play or hide main window components Tools group atoms measure align and superimpose structures and view and visualize data Applications set up submit and monitor jobs for Schr dinger s computational pro grams Some products have a submenu from which you can choose the task to be per formed Scripts manage and install Python scripts that come with the distribution and scripts that you create yourself See Chapter 12 of the Maestro User Manual for details Help open the Help panel and display or hide Balloon Help tooltips Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro 2 3 2 The Toolbar Button Types The main toolbar contains three kinds of buttons for performing common tasks ES Action Perform a simple task like clearing the Workspace aH Display Open or close a panel or open a dialog box such as the ER Project Table panel RA al Menu Display a button menu These buttons have a triangle in the lower right corner Types of Items on a Button Menu There are four types of items on button menus and all four types can be on the same menu see Figure 2 2 Action Perform an a
111. reactant and product structures Jaguar defines the forward direction using the rules described in Section 9 5 11 on page 192 You can also run an IRC scan from a point that is not a transition state by selecting Downhill from the Direction option menu and providing the geometry as if it were a transition state For these calculations you do not need an initial guess of the Hessian The scan follows the gradient from the initial point Downhill mode is set automatically in the restart file for an IRC job The default calculation generates 6 points in both forward and backward directions from the transition state at an interval of 0 1 in the reaction coordinate You can enter the number of points in the Number of IRC points text box and the step size in the IRC step size text box You can also limit the number of geometry optimization steps at each point in the Maximum optimization steps per point text box This value overrides any value set in the Optimization folder Finally for an IRC calculation Use mass weighted coordinates must be selected For an MEP calculation this option must be deselected When the calculation is finished the structures at the IRC or MEP points are automatically incorporated as separate entries in the Project Table and the reaction coordinate is incorpo rated as a property You can then sort the entries based on this property and display them in sequence using the ePlayer For an example
112. risk it is not recom mended as a permanent solution If you are using an SGI and you get an error message like this dgl error getservbyname unknown service sgi dgl tcp it means Jaguar is unable to find the SGI Distributed Graphics Library The file etc services should contain this information in a line beginning sgi dgl If this line is commented out that is if it begins with a character you can try uncommenting it If you continue to have this problem and it is affecting the GUI performance you should ask your system administrator for help 12 1 4 Problems Related to Your Temporary Directory When you run a Jaguar job Jaguar generates various files it needs during the calculation within a temporary directory often within a directory called scr tmp or something similar At the end of the job the program deletes most files in this directory by default copying back only the output file and any other files you requested If you get an error related to temporary directory space when you try to run Jaguar the program is probably having trouble getting access to the temporary directory space it needs to run If you are using Maestro to run jobs you can tell what temporary space Jaguar will try to use by looking at the Scratch directory setting in the Start dialog box The program actually makes a subdirectory named after the job within this directory and writes files there For instance if a person with the user name erwin
113. select either of the first two sources of job input the results of the calculations can be incorporated into the Maestro project If you run from structure files the results cannot be incorporated automatically You can select multiple structures as input for many kinds of Jaguar calculations When you do Maestro creates a Jaguar batch script that runs the calculation for each structure indepen dently These independent calculations can be run across multiple processors For more infor mation see Section 3 9 on page 46 Below the tabbed folders is the Job text box in which a summary of the calculation type is displayed and below this text box is a row of buttons Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Jaguar jaguar Silex Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Symmetry Use if present Molecular state v Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge Spin multiplicity 251 1 Basis set 6 31G Polarization s Diffuse None Number of D functions w 5D 6D 120 basis functions Start Read Write Edit Reset Close Help Figure 3 1 The Jaguar panel Start Opens a dialog box in which you can make selections for running the job and incorporating the output and then start the job See Section 3 9 on pa
114. setting the gen section keyword ipkat to either the atom s name or to the atom s order number in the zmat section Here are three equivalent input file examples for formic acid amp zmat C1 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H_pk 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp zmat Cl 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 22130316700 0 6129886300 0 3489813100 Hl 2 8258867600 0 1221771000 0 2269021000 Jaguar 6 0 User Manual 327 Chapter 14 The pK Prediction Module 328 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat H1 amp amp zmat C1 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 Hl 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat 4 amp When the pK job is run Jaguar checks that the functional group containing the designated pK atom has correction parameters available If it does not the job fails If you want to calculate a raw pK value using the Jaguar methods but without correction factors you can set ipkaraw 1 in the gen section of the input file 14 4 4 Running pK Calculations from the Command Line To submit a pK job for a single molecule using the co
115. several rsh commands on each of the hosts listed in the file machines LINUX and lists any prob lems If the command is successful it returns with no output You can also use the v option on the command line to see exactly what the script is doing Note Because MPICH uses rhosts authentication you must set up the rhosts file even if you are using ssh for communication 13 1 2 3 Launching the Secure Servers Jaguar relies on the MPICH secure server serv_p4 to transport the environment to all nodes used in a parallel calculation The secure server must be running on all computers on which Jaguar is to run in parallel which is normally all hosts listed in the machines LINUX file The secure server uses a communication port that is specified by the user or by root To launch the MPICH secure server enter the command SSCHRODINGER utilities mpich start p port Jaguar 6 0 User Manual Chapter 13 Parallel Jaguar The port number port should be a four digit number greater than 1023 If p port is not spec ified the value of MPI PASSPORT is used for the port number If MPI PASSPORT is not set the default value of 1234 is used Although each user may launch the secure server and select a port number for private use we recommend that the system administrator launch the server as root so that all users can use the same port number The port number should be different from the default 1234 to avoid conflicts with other uses of the s
116. significantly reduced if an NFS mounted scratch disk is used Also avoid using scratch directories which are actually symbolic links Using symbolic links for scratch directories is known to prevent Jaguar jobs from running especially under Linux Thus if scratch is actually a symbolic link to scr specify scr in the schrodinger hosts file rather than scratch 13 1 1 SGI Installation There are two system requirements for SGI a version of Message Passing Toolkit MPT no earlier than 1 6 0 0 and a version of Array Services no earlier than 3 5 These packages must be installed by the system administrator for your computer because the installation requires root permission Following are installation instructions 1 Check to see if the required MPI Message Passing Interface files are already installed with the command showprods grep MPI If MPI is not installed you can install it from the MPT package which can be down loaded from http www sgi com products evaluation 2 Install Array Services if it is not already installed You can check to see if Array Services is installed with the command showprods grep arraysvcs Array Services allows your SGI to run MPI applications like parallel Jaguar Start the array services daemon with the following command etc init d array start The arrayd daemon can be configured to start automatically at system startup with the command chkconfig array on Jaguar 6 0 User Manual
117. so that the final version is written either at the end of the run or just prior to any problems encountered 7 6 Generating Input Files for GAUSSIAN We recognize that some Jaguar users also use GAUSSIAN for calculations Therefore Jaguar can generate or read GAUSSIAN input files If you plan to perform GVB calculations with GAUSSIAN you may find this feature particularly useful since you can use Jaguar to generate a high quality GVB initial guess automatically You can use the GUI as a convenient tool to create GAUSSIAN input files The output file that is produced from the Jaguar run and whose name ends in gau can be used as a GAUSSIAN input Jaguar 6 0 User Manual 151 Chapter 7 Using Jaguar 152 file The gau file requests an HF or ROHF restricted open shell Hartree Fock calculation whichever is appropriate for the number of electrons in the system unless you choose to specify another method Details applying only to constructing an input file for a GVB calcula tion are discussed below To create a gau file select the Gaussian input file gau option in the Output folder If you are just creating a GAUSSIAN input file and you do not want to use Jaguar to generate a converged wave function you can save some time by choosing Initial Guess Only from the Jaguar submenu of the Applications menu or using the Edit Job dialog box to add the keyword setting igonly 1 initial guess only to the gen section of the input file
118. source and binary forms with or without modification are permitted for any purpose including commercial purposes provided that the following conditions are met 1 Redistributions of source code must retain the above copyright notice this list of condi tions and the following disclaimer 2 Redistributions in binary form must reproduce the above copyright notice this list of con ditions and the following disclaimer in the documentation and or materials provided with the distribution 3 In addition redistributions of modified forms of the source or binary code must carry prominent notices stating that the original code was changed and the date of the change 4 All publications or advertising materials mentioning features or use of this software are asked but not required to acknowledge that it was developed by the National Center for Supercomputing Applications at the University of Illinois at Urbana Champaign and to credit the contributors 5 Neither the name of the University nor the names of the Contributors may be used to endorse or promote products derived from this software without specific prior written permission from the University or the Contributors as appropriate for the name s to be used Maestro 7 0 User Manual 335 Appendix A Copyright Notices 336 6 THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY AND THE CONTRIBU TORS AS IS WITH NO WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED In no event
119. sss 102 Chapter Ge CEDE io a abis ida a Uic ine 105 6 1 Summarizing Jaguar Results sse 105 6 1 1 Reporting Final Results From One or More Jobs eeseesess 108 6 1 2 Reporting Intermediate Results ntt ea 109 6 1 3 Reporting Results for Each Atom eese 110 6 2 Output From a Standard HF Calculation s sss 110 Jaguar 6 0 User Manual Contents 6 3 Output File Content for Various Calculation Types 114 POMPE 115 6 3 2 EMP2Z ns ee 115 6 93 GN out LM xtti di eim IEEE lA toss os 116 6 3 4 Geometry or Transition State Optimization esses 117 6 325 SOlVatiOn a i ied ii etie sanatbelendey dads naeh 120 6 3 6 Geometry Optimization in Sol tlon oco erit ana 124 6 3 7 Properties Re LET 124 6 3 7 1 Multipole Moments and Charge Fitting essen 6 3 7 2 Polarizabilities and Hyperpolarizabilities eeeeeeeeeeeee 6 37 23 Electron Den anna 6 3 7 4 Mulliken Populations sirsenis iiavas neiaie 6 3 7 5 NBO Calculat ONS eii een 6 3 8 Frequency IR Intensity and Thermochemistry Output 6 3 9 CIS Calculations 6 3 10 Basis Selec ER 6 39 11 Methods EE 135 6 4 Options for Extra Output sss 135 6 5 File Output Options u44su2 30a Ra RAR pedes 138 6 6 Output O
120. storage scratch directories can be created such as scr or temp From this setting Jaguar creates a scratch directory named tmpdir userid jobname to store temporary files where userid is your account name on the execution host and jobname is the name of the Jaguar job For example if the user erwin ran a job named h2o on the host withi using the schrodinger hosts file Jaguar 6 0 User Manual 271 Chapter 11 Running Jobs 272 above the temporary directory used for the job would be temp erwin h2o By default Jaguar removes this subdirectory when the job is completed after copying back all important files to the output directory unless the subdirectory already existed when the job started You can override the tmpdir setting in the schrodinger hosts file by setting the SCHRODINGER TMPDIR environment variable For example if the directory designated by tmpdir becomes full with files that you don t have permission to delete you can set SCHRODINGER TMPDIR to a different directory and continue to run Jaguar jobs Instead of using tmpdir or SCHRODINGER TMPDIR you can directly specify the full path to the scratch directory in the JAGUAR SCRATCH environment variable 11 1 4 The processors Setting For stand alone computers with multiple processors set processors to the number of proces sors in the computer For computer clusters set processors for each node to the total number of processors in the entire cluster
121. the Jaguar programs run and a list of keyword settings including those made by default and program parameters This option is likely to be useful primarily for people who have a detailed knowledge of the code itself Memory disk and i o information The memory information provided by this option is given for most of the routines used during the run under the heading dynamic memory statistics Current and maximum values for the number of arrays their size in 8 byte words and their size in bytes as well as the type of vari 1 echo section constructed and keywords mtest 2 and ip24 2 in the gen section 2 Keyword ip5 2 in the gen section Jaguar 6 0 User Manual 135 Chapter 6 Output Jaguar jaguar ej ei x Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Write input files in the selected formats Extra detail to be written to output file Gaussian input file gau Echo input file and parameter list GAMESS input file gamess Memory disk and I O information Spartan archive file arc Detailed timing information XYZ file xyz Geometries in atomic units also Molden orbitals file molf Multipole moments in atomic units al At FS ee P m Orbital Coefficients Calculation stage At end of job After HF initial guess After SCF After final localization Each iteration in CO space Each iteration in AO space Orbitals
122. the commands in the batch script In this case there is no Jaguar 6 0 User Manual Chapter 11 Running Jobs template to be modified You can create the batch script and the Maestro input file from the Jaguar panels in Maestro and submit the batch job for execution or save the files to disk and run them later from the command line or from Maestro If you run remote batch jobs you should ensure that the input and output directories are on a disk system that is available to both the submission and the execution host such as a cross mounted disk or an NFS file system 11 3 3 Batch Input File Examples Batch scripts can be used in multiple ways In this section two examples are provided for the following scenarios 1 Pipelined scripts in which the output from one job provides the input to a subsequent job The pKa batch script is an example Here we provide an example that performs an opti mization at a medium level of theory followed by single point calculations at a higher level of theory 2 A script that uses the input files in one directory as templates and writes all new files into the launch directory This kind of script is useful for running jobs with different options on the same structure files 11 3 3 1 Pipelined Jobs Suppose you have ten different molecules and you want to optimize the geometry of each one at the B3LYP 6 31G level of theory and then do two single point energy calculations on the optimized geometry
123. the information for each atom follows The first line lists the atomic symbol for the atom followed by information which is simply a comment and is not read in The next line lists two numbers The first of these numbers gives the number of basis functions for that atom and basis set as listed in the default basis file and the second gives the number of electrons for that atom included in an effective core 0 for the basis sets whose names do not start with LA The line after that lists the orbital number 1 if it is the first orbital listed for that atom 2 if it is the second and so on the orbital occupation i e the number of electron pairs in that orbital and the orbital energy in Hartrees That orbital s coefficients for each basis function for the given atom and basis set s follow on the next line s When all of the orbitals for that atom have been specified a line with 4 characters indicates the end of the information for that atom and the data for the other atoms is listed Similar information for each other basis set follows If you want to set up your own atomig file you can do so if you use the format described above To use the file in a Jaguar calculation you must add a line saying ATOMIGFILE filename to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format host filename or user host filename 10 3 The Dealia
124. the next few sections Note The options listed in Table 11 2 and Table 11 3 apply to all Schr dinger programs not just to Jaguar Table 11 2 Information options for the jaguar command Option Description WHICH version args Show which version of jaguar and of the mmshare library would be used for the given version args LIST version args List the available versions of Jaguar that can be run on the specified host If no host is specified the local host is used If version args is ALL list all available versions of Jaguar even if not compatible with the specified host HOSTS List the hosts that are available for Jaguar calculations ENTRY Show the section of the schrodinger hosts file that will be used for this job WHY version args Gives information about why the specified version was selected Jaguar 6 0 User Manual Chapter 11 Running Jobs Table 11 3 Version options Option Description REL version Release version number v42 v4 2 42 v42062 41059 v4 1 049 are all acceptable forms VER pattern Pattern to match in the path to the executable Replaces v ARCH platform Platform code e g Linux IRIX mips4 11 2 1 Selecting an Execution Host If Jaguar is installed on several machines at your site you can use the jaguar command to help determine which host you should use to run your job To determine which local machines are available for running Jaguar jobs enter the command jagua
125. the number of processors for the job plus one because the Jaguar control program jexec always runs as a separate process Jaguar 6 0 User Manual Chapter 13 Parallel Jaguar Jaguar batch jobs cannot use MPI for the individual subjobs If you request multiple processors for a batch job with multiple input structures or files the subjobs are distributed over the avail able processors with one job per processor Jaguar 6 0 User Manual 307 Chapter 13 Parallel Jaguar 308 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module Schr dinger s pK prediction module represents the first attempt to use ab initio quantum chemical methods to reliably predict pK values in aqueous media 150 The module uses a combination of correlated ab initio quantum chemistry a self consistent reaction field SCRF continuum treatment of solvation and empirical corrections to repair deficiencies in both the ab initio and continuum solvation models This combination leads to high accuracy for a wide range of organic compounds in conjunction with tractable computational requirements The user interface has been designed to avoid the necessity of running the many individual jobs required to assemble the various components of the calculation Schr dinger has optimized each of the components for the best tradeoffs of accuracy versus efficiency The empirical correction terms which have been developed for ionizable groups relevant to the
126. to i the row indicator are then read in one row at a time Each row of five or fewer matrix elements starts with an arbi trary integer label this integer is not used in the program but can be used to label the row for example When the relevant matrix elements from that entire five column block have been read in the next block is read in the same way until all of the matrix elements for the lower triangle of the matrix have been entered For example in the unlikely event that you wanted to enter this Hessian 11 21 31 4 51 61 71 8 21 22 32 42 52 62 72 82 3Q 32 3 43 53 03 73 8 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File 41 42 13 4 54 064 74 84 51 2 53 54 55 65 75 85 61 62 63 64 65 66 76 86 71 72 3 74 75 76 77 87 81 82 83 84 85 86 387 88 you would need to enter the elements from the bottom triangle of the Hessian shown in bold in the following way amp hess j Ei 11 i 21 22 i 31 32 33 i 41 42 43 44 i 541 52 53 54 55 i 61 62 63 64 65 i 71 T2 73 74 75 i 81 82 83 84 85 j i 66 i 76 77 i 86 87 88 amp where i and j indicate integer labels not actually used by the program 9 10 The guess Section If an input file has a non empty guess section the keyword iguess in the gen section is set to 1 and an initial guess for the wave function is read from the guess section If the label basgss is given the coefficients given in the guess section are interpreted as coefficients of functions fro
127. version of the program the user must make this correction by hand to the result obtained from running the pK prediction module The correction factor is log N where N is the number of equivalent sites and the power of 2 comes from the fact that there are two particles involved H and the species being protonated The correction factors for two and three equivalent sites 298 K are 2equivalent sites bases 0 60 acids 0 60 e 3 equivalent sites bases 0 95 acids 0 95 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module 14 2 3 Multiple Protonation Sites Many molecules have several sites which can have different pK values Consider a case with two distinct possible protonation sites for which we want to calculate the pK of site 1 Then the following situations are possible 1 The two pK values are well separated and the pK of site 1 is higher than that of site 2 In this case site 2 will be deprotonated when site 1 is being titrated in an experiment The pK calculation for site 1 is run with site 2 in the deprotonated state 2 The two pK values are well separated and the pK of site 2 is higher than that of site 1 In this case site 2 will be protonated when site 1 is being titrated in an experiment The pK calculation for site 1 is run with site 2 in the protonated state 3 The two pK values are unknown or the pK values are close together In this case there are a total of four protonation sta
128. with HF wave functions For open shell systems you can perform gas phase energy and geometry optimizations but not property calculations All local MP2 geometry optimizations employ analytic gradients For calculations of LMP2 dipole moments Jaguar computes a coupled perturbed Hartree Fock CPHF wave function which can be computationally expensive However since CPHF methods lead to a better description of the charge density we recommend computing LMP2 dipole moments as well for any calculation for which you need to compute accurate LMP2 31 Keyword dftname mpwl1pw91 in the gen section 32 Keyword icis 1 in the gen section 33 Keyword nroot in the gen section 34 Keyword maxciit in the gen section 35 Keyword mp2 3 in the gen section Jaguar 6 0 User Manual 63 Chapter 4 Options 64 electrostatic potential ESP fitted charges For details see Section 4 10 1 on page 74 and Section 4 10 3 on page 76 Jaguar s implementation of the local MP2 method requires basis sets that allow the pseudo spectral method to be used This basis set information can be found in Section 4 2 on page 55 A warning is displayed if you choose a non pseudospectral calculation The reference wave function is produced through a localization of the usual Hartree Fock reference wave function using a unitary transformation of the occupied canonical Hartree Fock orbitals This localization procedure does not change the reference energy
129. with no contradiction If no such matching description exists in the Lewis file the atom is assigned the default radius for that element Atom type descriptions in the Lewis file should be preceded by a heading beginning RADII TYPE 01 for information applying to HF GVB or DFT wave functions or RADII TYPE 02 for information for LMP2 wave functions After that each atom type description is listed Blank lines are allowed in an atom type description list and as long as some spacing exists between numbers and comments on each line the number of spacing characters is irrelevant However keep in mind that the order of the atom type descriptions is important since the first matching description will always be used Each line describing an atom type has six integers one real number and an optional comment in that order The integers describe the atom type while the real number sets the radius in angstroms for that atom type The six integers describe the following characteristics in turn Atomic number for instance 6 for carbon Hybridization of the atom itself Bonding type of the atom elements it is bound to and order of those bonds Hybridization type of the atom hybridization and elements of atoms to which it is bound Size of ring if any the atom is in Aromaticity of that ring according to Huckel Rule aromatic rings have 4n 2 pi elec trons where n is a non negative integer Jaguar 6 0 User Manual
130. x 0 000 beta y y y 0 000 beta z z z 10 206 beta x y y 0 000 beta x z z 0 000 beta y x x 0 000 beta y z z 0 000 beta z x x 0 435 Md y y 0 404 beta x y z 0 000 sum beta x 0 000 sum beta y 0 000 sum beta z 9 367 beta 5 620 second hyperpolarizability in AU gamma x x x x 9 110 gamma y y y y 11 758 gamma z z z z 28 020 gamma x y 0 000 gamma x x x z 0 000 gamma x x y y 1780 861 gamma x x y z 0 000 Jaguar 6 0 User Manual Chapter 6 Output gamma x x z z 2 950 gamma x y y y 0 000 gamma x y y z 0 000 gamma x y z z 0 000 gamma x z z z 0 000 gamma y y y z 0 000 gamma y y z z 2 5 235 gamma y z z z 0 000 gamma 718 848 After the tensor matrix elements the program prints various sums of these matrix elements For the polarizability the quantities and Ao are reported as alpha and Dalpha defined as follows a 0 0 0 3 2 2 2 AQ Ka 0 0 Azz OQ 0 For the first hyperpolarizability three sums are reported which are defined by the following expression IP Baxx Boy Bazz where q can be x y or z The average hyperpolarizability D is defined by p s EB tu Ep up where u is the dipole moment The average second hyperpolarizability y is defined by 1 Y PDT p 4 where p and q run over the three coordinates x y and z 6 3 7 3 Electron Density If you choose to calculate the electron de
131. 0 020561 M0 222 0 050 benzene_dft 01 benzene orb JMO 23 E 0 020551 MO 23 0 05 Isovalue EE SEED 0 05 Import Duplicate Delete Limit Display Options Quick Start Guide Jaguar 6 0 User Manual Figure 4 12 The Surface Table panel For a tutorial guide to generating and displaying orbital surfaces see Section 3 6 of the Jaguar isplay Options 0 Transparency I 0 Style 4 Solid Mesh w Dot Color scheme v Property Constant Color Red Negative color v Map values from volume data OK Apply Cancel Help Figure 4 13 The Display Options dialog box Chapter 5 Optimizations and Scans For Hartree Fock GVB LMP2 and DFT calculations in gas phase or in solution Jaguar can use calculated analytic gradients to optimize the molecular geometry to a minimum energy structure or a transition state In addition to locating stationary points Jaguar can calculate points along one or more coordinates with or without optimizing the other coordinates These scans include intrinsic reaction coordinate IRC and minimum energy path MEP scans as well as geometry scans of specified coordinates There are five tasks on the Jaguar submenu of the Applications menu that support optimiza tions and scans Optimization Relaxed Coordinate Scan Rigid Coordinate Scan Transition State Search Reaction Coordinate Throughout this chapter footnotes in
132. 0 555133 Occupation 021223773328496 0 000000000000000 004301782758377 0 000000000000000 003952404680376 0 003763985866478 000000000000000 0 000000000000000 000000000000000 0 000372571507087 000343482092802 0 000000000000000 1 345597 Occupation 471018758398392 0 000000000000000 417774726334513 0 000000000000000 001405346737926 0 006172871870042 000000000000000 0 000000000000000 000000000000000 0 022047889711935 013067257872503 0 000000000000000 For the Format option All elements as f8 5 in list 0 99466 0 02122 0 00000 0 00395 0 00376 0 00381 0 0 00037 0 00025 0 00000 0 1 Orbital Energy 2 Orbital Energy xl 21055 0 47102 0 00000 0 0 00141 0 00617 0 00819 0 02205 0 01342 0 14851 0 20 555133 Occupation For the Format option All elements as e15 6 in table 25 1 9 946611E 01 2 122377E 02 1 550432E 03 4 301783E 03 988566E 06 988566E 06 2 520402E 04 2 2 105494E 01 4 710188E 01 oo 586249E 02 4 177747E 01 1 485137E 01 1 485137E 01 1 341957E 02 6 7 The Log File The log file an output file which appears in the local job directory provides information on the progress of a run The current contents of a job s log file is displayed in the Monitor panel The log file notes when each program within Jaguar is complete as well as noting data from each SCF iteration The data from the SCF iterations is shown in table form Some of the text for the 3 column he
133. 0 6 20 6 85 56 95 18 20 reduc mass 5 96 4 34 4 66 7 85 4 37 4 40 force const 18 88 1 38 4 57 2491 3 06 F1 X 03713 07085 05263 01504 10332 10413 F1 Y 07738 08093 07570 00294 00858 01121 F1 Z 11257 01960 00381 00291 00007 00142 02 X 03630 04451 02646 05071 13148 12893 02 Y 00653 00113 11356 16823 01169 04865 02 Z 07806 12275 08708 00749 00934 01566 03 X 07467 12140 11117 03829 00279 01163 03 Y 02320 01992 07655 17175 02320 01800 03 Z 03681 04285 05472 00584 13452 13276 FA X 13055 00611 01869 00459 00502 00537 FA Y 05236 09865 08436 00590 01826 01460 FA Z 01586 04767 03106 01413 10532 10001 Thermochemical properties at 1 0000 atm rotational symmetry number 1 rotational temperatures K 1 075181 283392 256070 vibrational temperatures mode 1 2 3 4 5 6 temp K 326 36 844 73 1019 03 1430 30 1529 51 1563 02 Thermodynamic properties calculated assuming an ideal gas In the table below the units for temperature are kelvins the units for U H and G are kcal mol and the units for Cv and S are cal mol K The zero point energy ZPE 6 670 kcal mol is not included in U H or G in the table below Jaguar 6 0 User Manual Chapter 6 Output TS 298 15 K U Cv S trans 889 2 981 38 655 rot 889 2 981 23 636 vib 558 4 662 2 907 elec 000 000 000 total 2 335 10 623 65 198 Total internal energy Utot S
134. 0 Do not do IRC calculation 1 Do IRC calculation with non mass weighted coordinates minimum energy path scan 2 Do IRC with mass weighted coordinates ircmode forward Find IRC points in forward direction from the transition state reverse Find IRC points in reverse direction from the transition state downhill Find IRC points by moving downhill from an initial geometry that is not a transition state both Find IRC points in both forward and reverse directions from the transition state ircmax 6 Maximum number of IRC points to be found in any direction Must be a positive integer iremxcyc 30 Maximum number of geometry iterations to calculate each IRC point Must be a positive integer ircstep 0 1 Step size taken for each IRC point in bohrs amu or radians amu ircgcut 1 0 Scale factor for the cutoff that is used to determine whether the gradient is too small to locate the next IRC point ip472 0 Do not save the IRC structures in the mae output file 2 Save the IRC structures in the mae output file and write the reaction coordinate value as a property Jaguar 6 0 User Manual 193 Chapter 9 The Jaguar Input File 194 IRC in anything but the downhill mode requires a Hessian which must either be entered in the hess section or calculated analytically The latter is specified with inhess 4 in the gen section Initial guess Hessians are not useful as they do not have any imaginary frequencies If a Hessian
135. 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 describes a water molecule Each atomic label must start with the one or two letter element symbol and may be followed by additional characters as long as the atomic label has eight or fewer characters and the atomic symbol remains clear For example HE5 would be interpreted as helium atom 5 not hydrogen atom E5 The atom label is case insensitive The coordinates may be specified in any valid C format but each line of the geometry input should contain no more than 80 characters 3 4 2 Variables in Cartesian Input Coordinates can also be specified as variables whose values are set below the list of atomic coordinates This makes it easier to enter equal values and also makes it possible to keep several atoms within the same plane during a geometry optimization To use variables type the variable name zcoor for instance where you would normally type the corresponding numerical value for each relevant coordinate You can prefix any variable with a or sign When you have entered the full geometry add one or more lines setting the variables For instance the Cartesian input Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 describes the same water coordinates as the previous Cartesian input example If you performed a geometry optimization using this input structure its ycoor and zcoor values might change b
136. 04 in transition state search 94 specifying in input file 171 specifying in Maestro sese 95 reading input files troubleshooting 294 redundant internal coordinates 90 keyword 187 suppression of use 37 relativistic effects 57 58 resonance in GVB calculations esses 67 in GVB LMP2 calculations 67 in LMP2 calculations sssss 65 RESP file keyword 215 restarting calculations 150 151 GVB 225 Gt al 8UESSL ai S Aceh 146 Jaguar 6 0 User Manual restart file citare 214 215 with improved guess n 149 restricted open shell wave functions Ia M 202 Maestro setting eee 59 63 results summary of 105 110 I E sera 108 for EACH atomi titer 110 1intermediate eee tienen 109 RFO level shifting keyword for 189 rhosts file use with MPICH 300 Run Batch File panel sss 50 running jobs from Maestro essssss 30 31 46 52 from the command line 275 277 multiple 49 51 on a remote host eerte 277 troubleshooting sess 289 294 RvR information keywords for output of 213 EWE PLO ST AM ges Er
137. 11 Project Table panel sess 12 in 14 mouse functions 16 17 Shortc t keys erre treten 17 PLOJOCHS P 11 properties ESP charge fitting ss 74 76 IR intensities eennsesesnenesnennennnnennennnnnn 83 Jaguar 6 0 User Manual 357 Index 358 keywords entrer 196 199 Mulliken population analysis 76 multipole moments eeeereteee 76 NMR shielding constants da MIR 74 84 QUIDUL nee er 124 129 polarizability and hyperpolarizability 77 thermochemical sss 83 84 Properties folder 775 18 80 85 pseudospectral method 155 157 publications citing Jaguar in eee 2 Python scripts see scripts Q QST guided transition state searches 93 94 additional structures for 171 172 key WOT icto tox tic ten ntis 188 LMP delocalization for 179 226 quadratic energy error output keyword 213 quadratic synchronous transit see QST guided transition state searches quitting Maestro eene 28 31 R radian units for geometry input 175 radius covalent ec rr Re it ertet ri 229 van der Waals reete 229 reactant geometry for IRC calculations sss 1
138. 11 2 The jaguar Command You can use the jaguar command to perform the following tasks among others e Runa job on any machine at your site with any installed version of Jaguar Kill a Jaguar job that you started on any machine at your site Listthe machines on which Jaguar is installed List the jobs that are running on a particular machine If Jaguar is installed on more than one machine at your site you can use the jaguar command on one machine to run kill or list Jaguar jobs on another machine even if you are not logged in to the second machine This section describes in some detail how and when to use the jaguar command The syntax of the jaguar command is jaguar command options where command is any of the commands listed in Table 11 1 The options may be given in any order and may precede any options specific to the command The jobnames argument to the jaguar command is a list of names Each name in the list is the name of a Jaguar job that is run and each name also specifies an input file The name can be given with or without a in extension If the in extension is given Jaguar removes it to form the job name If the in extension is not given Jaguar adds it to form the input file name Jaguar 6 0 User Manual Chapter 11 Running Jobs Table 11 1 Commands for the jaguar command Command Description run version args runargs jobnames batch batch options script jobnames pka jobnam
139. 14 10000000D 01 56164871D 15 78183836D 15 26536093D 14 9 11 The pointch Section The pointch section describes the locations and magnitudes of a set of point charges Up to 200 000 point charges may be used Each line of the pointch section should contain four real numbers the first specifying the point charge in atomic units and the next three specifying its x y z coordinates in the same units used for the geometry angstroms by default but bohrs if the iunit keyword in the gen section is set to 0 or 2 see Section 9 5 1 on page 174 for more information Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File The sample pointch section below puts one point charge of charge 1 at location 0 0 0 2 and another of charge 1 at location 0 0 0 4 amp pointch 1 0 0 0 0 2 1 0 0 0 0 4 amp Note that point charges should nor contribute to the value of the net molecular charge molchg given in the gen section If you include a non empty pointch section in the input file for a job the output from the program pre includes a table of fixed charge information describing the point charges This table appears in the output file immediately after the molecular geometry output 9 12 The efields Section If you would like to calculate wave functions or molecular properties in the presence of an electric field you may use the efields section to describe this field The x y and z components of the electric field sh
140. 2 or DFT results A substitution of a specified number or character string for one already in the template input file Jaguar 6 0 User Manual Chapter 11 Running Jobs The format for each of these options and an example of each kind are shown in Table 11 7 Option assignments must not have spaces around the or operators Host names cannot be included in any of the paths described in the table You should avoid using any of the charac ters lt gt in a substitution pattern These options and the other line types in a batch input file are illustrated in the sample files in the next subsection Directions on how to submit a batch job follow in the final subsection Table 11 7 Definition of options that are applied to a template file to generate an input file Change Format Examples set keywords keyword new value or key basis lav3p word NONE to remove a setting dftname b3lyp igeopt NONE specify a data file path filetype fullpathname or file BASISFILE usr es and name type NONE to return to default my bas choice for that file type ATOMIGFILE NONE DAFFILE NONE GRIDFILE NONE CUTOFFFILE NONE GPTSFILE NONE WAVEFNFILE NONE remove a section RMSECTION section name RMSECTION guess RMSECTION gvb clear the gen section RESETGEN except for the multip and molchg settings insert a file at the top of ADDTOP filename ADDTOP guess in the input append a fi
141. 3 21 1 0e 3 22 3 0 24 1 0e 2 means that jcor is 5 kcor is 2 the ultrafine grid is used and that three cutoff values which differ from the defaults follow The next three lines set the cutoff values cut21 cut22 and cut24 If you need more information on cutoffs contact Schr dinger The variables jcor and kcor determine what analytic corrections are calculated for a particular SCF iteration The meanings of their possible values are shown in Table 10 2 The variables a b and c in the table refer to distinct atoms Table 10 2 Determination of calculations of analytic corrections for SCF iterations Variable Value Description jcor 0 No Coulomb terms calculated analytically 1 Atomic analytic corrections of the form lt aalaa gt calculated for J 3 Analytic corrections of the form aalaa and aalbb calculated for J 4 Analytic corrections of the form aalaa aalab aalbb and aalbc calculated for J 5 Analytic corrections of the form aalaa lt aalab gt lt aalbb gt lt ablab gt and lt aalbc gt calculated for J diatomic lt aalbc gt kcor 0 No exchange terms calculated analytically 1 Atomic analytic corrections of the form lt aalaa gt calculated for K 2 Diatomic analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt and lt ablab gt calculated for K a a b and c refer to distinct atoms To perform an all analytic calculation you can set the keyword nops in the gen s
142. 3 etot 3 Y N 6 M 76 03617415619 2 0E 05 0 0E 00 0 0E 00 Jaguar 6 0 User Manual 121 Chapter 6 Output 122 Energy components in hartrees A Total zero electron terms 9 35161183359 B Nuclear nuclear 9 33000672144 C Nuclear solvent 2 0 02160511215 E Total one electron terms 123 39806065860 F Electron nuclear 199 21812919134 G Electron solvent 0 03443064237 H KinebilC seine te aAA ade 75 85449917511 I Total two electron terms 38 01027466882 L Electronic energy 85 38778598978 E I N Total quantum mech energy 76 03617415619 A L O Gas phase energy 76 02364072535 P Solution phase energy 76 02607108661 Q R S Q Total solute energy 76 02334862596 N C G R Total solvent energy 0 00641276511 C 2 G 2 S Solute cavity energy 0 00369030447 U Reorganization energy 0 00029209939 Q O V Solvation energy 0 00243036126 P O SCFE SCF energy HF 76 03617415619 hartrees iterations 3 HOMO energy 0 49985 LUMO energy 0 22469 Orbital energies symmetry label 20 55803 A1 1 34624 A1 0 71287 B2 0 57176 A1 0 49985 B1 0 22469 A1 0 31901 B2 1 01892 B2 1 09275 A1 1 13045 A1 1 16509 B1 1 29393 B2 1 41452 A1 1 80375 A2 1 82851 A1 end of program scf As for any later solvation iterations the sc output begi
143. 5 K including the SCF energy and zero point energy pK pK total dipole moment Geometry optimization options iterg stepg zvar name grms gmax drms dmax echange geopt iteration number geopt step number z variable value must be followed by zvar name rms gradient maximum gradient component rms displacement maximum displacement energy change Jaguar 6 0 User Manual 107 Chapter 6 Output 108 Table 6 1 Options for the jaguar results command Continued Option Meaning Timing options time total cpu time for job tscf total time in sc f cumulative trwr total time in rwr cumulative tderlb total time in der1b cumulative SCF information options iter number of scf iterations Per atom information options atoms atom names atomnums atomic numbers coords cartesian atomic coordinates forces cartesian atomic forces charges ESP atom centered charges Options for printing of title and intermediate results title print column titles titleonly print only the column titles all report results every geometry iteration allscf report results for each scf calculation allderib report results for each der1b 6 1 1 Reporting Final Results From One or More Jobs By default each row of the Jaguar results table except the title row corresponds to the final results from a Jaguar output file that was listed in the jaguar results command For instance if you entere
144. 6 vwn5 in the gen section Keyword dftname pwpw9l in the gen section Keyword dftname pbe in the gen section Jaguar 6 0 User Manual 61 Chapter 4 Options 62 HCTH407 Hamprecht Cohen Tozer Handy functional including local and nonlocal exchange and correlation reparametrized with a training set of 407 molecules by Boese and Handy 40 Hybrid Functionals 20 21 22 23 24 25 26 27 28 29 30 B3LYP Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Lee Yang Parr local and nonlocal functional 33 See refs 27 and 28 B3PW917 Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gradi ent correction 32 correlation Perdew Wang 1991 local and GGA II nonlocal func tional 31 B3P86 Exchange exact HF Slater local exchange functional 29 Becke 1988 nonlo cal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Perdew 1986 nonlocal gradient correction 35 B97 1 Reparametrization of Becke s 1997 hybrid functional 36 by Hamprecht Cohen Tozer and Handy 39 B98 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 37 SB98 Schmider and Becke reparametrization of Becke s 1998 functional 38 BHandH 50 exact HF exchange 50 Slater local e
145. 6840 Lajohn L Christiansen P A Ross R B Atashroo T Ermler W C J Chem Phys 1987 57 2812 Jaguar 6 0 User Manual References 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 Ross R B Powers J M Atashroo T Ermler W C Lajohn L Christiansen P A J Chem Phys 1990 93 6654 Ross R B Gayen S Ermler W C J Chem Phys 1994 100 8145 Ermler W C Ross R B Christiansen P A Int J Quantum Chem 1991 40 829 Nash C S Bursten B E Ermler W C J Chem Phys 1997 106 5133 Wildman S A DiLabio G A Christiansen P A J Chem Phys 1997 107 9975 Diffuse and polarization functions for Ga Rn taken from Dyall K G Theor Chem Acta 1998 99 366 diffuse functions for rare gases extrapolated from those for the other elements in the row Hamilton T P Pulay P J Chem Phys 1986 84 5728 Pulay P J Comput Chem 1982 3 556 Pulay P Chem Phys Lett 1980 73 393 Obara S Saika A J Chem Phys 1986 54 3963 Gill P M W Head Gordon M Pople J A J Chem Phys 1990 94 5564 Gill P M W Head Gordon M Pople J A Int J Quantum Chem 1989 S23 269 Head Gordon M Pople J A J Chem Phys 1988 89 5777 Murphy R B Messmer R P J Chem Phys 1993 98 10102 For information on Molden see the Molden web site http w
146. 69700000000000 6 838450000000000E 02 6 360000000000000E 02 1 01405500000000 P 4 1 0 2 040000000000000E 02 1 00000000000000 kk Na 2 10 D_AND_UP 1 175 55025900 10 00000000 2 35 05167910 47 49020240 2 7 90602700 17 22830070 2 2 33657190 6 06377820 2 0 77998670 0 72993930 S D 0 243 36058460 3 00000000 1 41 57647590 36 28476260 2 13 26491670 72 93048800 Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files 2 3 67971650 23 84011510 2 0 97642090 6 01238610 P D 0 1257 26506820 5 00000000 1 189 62488100 117 44956830 2 54 52477590 423 39867040 2 13 74499550 109 32472970 2 3 68135790 31 37016560 2 0 94611060 7 12418130 KKK 10 1 3 Customizing Basis Sets If you want to set up your own basis file you can do so if you use the format described above Generally you must also create an altered version of the atomig file which is described in Section 10 2 although if you are just adding polarization functions to the basis set and these functions are identified by the polarization diffuse function parameter described earlier in this section you can continue to use the usual atomig file Make sure your new basis file contains the 6 31G basis set because the initial guess program needs this basis set If you alter the basis functions in the default basis file only slightly you can use the same names for the basis sets If you change them a great deal you should use a new name so that Jaguar will not attempt to use gri
147. 9 0 5 guanidine 12 8 13 6 0 8 methylguanidine 13 7 13 4 0 3 PYRROLES C 2 protonation pyrrole 3 9 3 8 0 1 1 methylpyrrole 2 8 2 9 0 1 2 methylpyrrole 0 5 0 2 0 3 3 methylpyrrole 0 7 1 0 0 3 INDOLES C 3 protonation indole 3 7 3 6 0 1 methylindole 2 0 2 3 0 3 2 methylindole 0 4 0 3 0 1 3 methylindole 4 6 4 6 0 0 324 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module 14 4 Running pK Calculations pK calculations consist of a calculation on the protonated form and a calculation on the depro tonated form of the target molecule with an empirical correction The calculations are performed using a Jaguar batch script You need only supply an input file with the acidic or basic atom marked and use the batch script to run the calculation You can set up pK calcula tions in Maestro or prepare the input files in a text editor and submit the jobs from the command line 14 4 1 Activating the pK Module To run the pK module you need a special license in addition to the regular Jaguar license To install the pK module first install Jaguar using the instructions in the Schr dinger Product Installation Guide After you have successfully installed Jaguar send in the machid informa tion to obtain a license to activate the pK module Explicitly indicate in your license request that you want to run pK calculations 14 4 2 Running pK Calculations from Maestro To set up and submit pK ca
148. 94 135 3 12 3 U3 3 1 McLaren p 296 135 4 14 5 Un 5 2 Albrecht amp Collatz p 294 135 5 18 5 Un 5 1 Albrecht amp Collatz p 294 135 6 18 5 Un 5 1 Albrecht amp Collatz p 294 135 7 24 5 Un 5 4 Stroud p 295 135 8 26 7 Un 7 1 Albrecht amp Collatz p 295 135 9 38 9 9 1 Lebedev 136 10 38 9 9 1 Lebedev 136 11 42 9 9 2 Lebedev 136 12 44 9 9 3 Lebedev 136 Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files Table 10 1 Number of points per angular shell and degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line Continued Entry Points Degree Reference for Grid 13 44 9 9 4 Lebedev 136 14 50 11 U3 11 1 McLaren p 301 135 11 1 Lebedev 136 15 54 11 11 2 Lebedev 136 16 56 11 U3 11 2 Stroud p 301 135 17 60 11 11 3 Lebedev 136 18 60 11 11 3 Lebedev 136 19 78 13 13 2 Lebedev 136 20 78 13 13 3 Lebedev 136 21 86 15 15 1 Lebedev 136 22 90 15 15 2 Lebedev 136 23 90 15 15 2 Lebedev 136 24 110 17 17 1 Lebedev 136 25 116 17 17 2 Lebedev 136 26 146 19 19 Lebedev 137 27 146 19 19 Lebedev 137 28 194 23 23 Lebedev 137 29 302 29 29 Lebedev 138 30 434 35 Lebedev 139 10 5 The Cutoff File The cutoff file specifies parameters to be used for the various iterations of an SCF calculation The file to be used is determined by the CUTOFFFILE entr
149. 944 1 000000 3 116944 Y 4 1 000000 3 116944 Z 5 1 000000 3 116944 Oo 11 x 3 3 599934 2 401438 1 000000 2 401438 Y 4 1 000000 2 401438 Z 5 1 000000 2 401438 Oo 12 X 3 1 013762 1 054360 1 000000 1 054360 Y 4 1 000000 1 054360 Z 5 1 000000 1 054360 Oo 13 S 6 0 270006 0 266956 1 000000 0 266956 Oo 14 x 7 0 270006 0 277432 1 000000 0 277432 Y 8 1 000000 0 277432 Z 9 1 000000 0 277432 Oo 15 XX 10 0 800000 1 113825 1 000000 1 113825 Yy dd 1 000000 1 113825 ZZ 12 1 000000 1 113825 XY 3 1 732051 1 929201 XZ 14 1 732051 1 929201 YZ 15 1 732051 1 929201 H1 1 S 16 18 731137 0 214935 1 000000 0 214935 H1 2 S 16 2 825394 0 364571 1 000000 0 364571 H1 3 S 16 0 640122 0 415051 1 000000 0 415051 H1 4 S 17 0 161278 0 181381 1 000000 0 181381 H1 5 X 18 1 100000 1 605761 1 000000 1 605761 Ys 19 1 000000 1 605761 Z 20 1 000000 1 605761 H2 1l 8 21 18 731137 0 214935 1 000000 0 214935 H2 2 S 21 2 825394 0 364571 1 000000 0 364571 H2 3 S 21 0 640122 0 415051 1 000000 0 415051 H2 4 S 22 0 161278 0 181381 1 000000 0 181381 H2 5 X 23 1 100000 1 605761 1 000000 1 605761 Y 24 1 000000 1 605761 Z 25 1 000000 1 605761 134 Jaguar 6 0 User Manual Chapter 6 Output The table is followed by a list indicating the number of electrons in each atom that are treated with an effective core potential 6 3 11 Methods If the DIIS convergence method is not used the maximum DIIS error column is not printed for the table giving data from the SCF iterations Also if
150. A III Chapter 4 In Modern Theoretical Chemistry Methods of Electronic Structure Theory Schaefer H F III Ed 3 Plenum New York 1977 BIOGRAF manual MacroModel manual Frisch M J Trucks G W Head Gordon M Gill P M W Wong M W Foresman J B Johnson B G Schlegel H B Robb M A Replogle E S Gomperts R Andres J L Raghavachari K Binkley J S Gonzalez C Martin R L Fox D J DeFrees D J Baker J Stewart J J P Pople J A GAUSSIAN 92 Gaussian Inc Pittsburgh PA 1992 Jaguar 6 0 User Manual References 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 Babel version 1 6 copyright 1992 96 W Patrick Walters and Matthew T Stahl AII Rights Reserved Permission of authors granted to incorporate Babel into Jaguar Dunietz B D Murphy R B Friesner R A Calculation of enthalpies of formation by a multi configurational localized perturbation theory application for closed shell cases J Chem Phys 1999 110 1921 Becke A D J Chem Phys 1993 98 1372 Becke A D J Chem Phys 1993 98 5648 Stephens P J Devlin F J Chabalowski C F Frisch M J J Phys Chem 1994 96 11623 Slater J C Quantum Theory of Molecules and Solids Vol 4 The Self Consistent Field for Molecules and Solids McGraw Hill New York 1974 Vosko S H Wilk L Nusair M Can J Phy
151. CFE ZPE end of program freq U Total enthalpy H Utot pV Total Gibbs free energy H T S 348 348 348 16 511 203415 hartrees 202471 hartrees 233448 hartrees If infrared intensities were calculated several additional programs are run after the first run of the program scf These programs compute the derivatives of the dipole moment which are needed to calculate the IR intensities The IR intensities are listed in the frequencies table described above 6 3 9 CIS Calculations Output from CIS calculations of excited states lists the selected excited states with the excita tion energy from the ground state in eV and the transition wavelength the orbital excitations involved in the CI wave function and the transition dipole moment and oscillator strength The following example is for H O Excited State 1 9 3904 eV 132 03 nm orbitals in excitation CI coeff 5 gt 6 0 95735 5 gt 11 0 26823 Transition dipole moment debye X 0 0000 Y 1 3726 Z 0 0000 Tot 1 3726 Oscillator strength f 0 0671 Excited State 2 11 5077 eV 107 74 nm orbitals in excitation CI coeff 5 gt 7 0 82270 5 gt 10 0 55056 5 gt 14 0 11504 Jaguar 6 0 User Manual 131 Chapter 6 Output 132 Transition dipole moment debye X 0 0000 Y 0 0000 Z 0 0000 Tot 0 0000 Oscillator strength f 0 0000 From this example the lowest excited state of water is mostly a transiti
152. Chapter 3 Running Jaguar From Maestro names of the input output and log files for your job depend on the name you provide the Jaguar input file is named jobname in the output file is named jobname out and the log file is named jobname 10g where jobname is the text that appears in the Name text box The default execution host the machine that the job will run on is selected in the Host option menu This default is localhost which means the machine on which Maestro is running The host name is followed by the number of available processors in parentheses If Jaguar is installed on more than one machine at your site you can change the choice of execution host by selecting another host from the option menu The Scratch directory option menu displays the directory on the execution host that will be used during the calculation to store temporary files You should check that the directory already exists on the execution host If it does not exist you should create it You should not need to change any other settings Click the Start button to start the job After you start the job the Monitor panel is displayed see Figure 2 7 on page 27 This panel is auto matically updated to show the progress of your job As each separate program in the Jaguar code finishes running its completion is noted in the log text area When the program scf is running the Monitor panel displays the energy and other data of each iteration See Section 6 7 on
153. Chapter 8 GVB calculations include what is sometimes called non dynamical electron correlation To run a GVB calculation you must define atom pairs and orbital types that you want to be treated with the GVB method In the GVB Pairs section of the Theory folder you can select All atom pairs or Heteroatom pairs Heteroatom pairs include all atom pairs except C atoms bonded only to C and H atoms If you compute solvation energies using GVB or LMP2 as Jaguar 6 0 User Manual Chapter 4 Options described in Section 4 9 on page 71 we recommend using heteroatom pairs for the GVB calculation for the most efficient results since solvation energy calculations often use radii optimized for calculations with heteroatom pairs set See Section 10 6 on page 260 for more details If you want to select other pairs you can do so by adding a gvb section to the input file If you add a gvb section the Level of theory is set to Other The GVB method in Jaguar does not include the concept of resonance Consequently the GVB pair input for a molecule such as benzene for example should include alternate single and double bonds for its carbon ring If you perform a GVB geometry optimization on a molecule with equal resonating bonds like the carbon bonds in benzene you should force the opti mizer to keep their bond distances the same even if the input lists different bond orders for the bonds To impose this restriction use Z matrix form for you
154. D eee 276 Theory folder sss 60 65 66 thermal smearing 70 205 thermochemical properties 83 84 keywords eire eene thor 200 uM M 130 Jaguar 6 0 User Manual 359 Index 360 time stamps in log file option for 276 timex progratm eene ect es enne et nno 240 timing information key WOT i een tete nnns 213 Maestro option see 136 toolbar Build panel htt 20 21 main window seseeeeren 7 10 Project Table panel 13 14 torsional angles freezing Alias 188 ID Zee TAWA en nenn bei 38 transition metals improving convergence 69 147 148 initial guess for 145 146 148 234 Transition State folder 94 transition vector 95 192 transition state optimization 87 98 constraining bond lengths or angles 90 93 convergence criteria coordinate system eigenvector following 97 188 frozen bond lengths or angles 90 93 in solution esssesseeeeeereee 73 186 initial Hessian 40 41 89 90 97 98 171 189 keywords ntn tnn 186 191 level shifting of Hessian 189 limiting step size for 190 191 maximum iteratio
155. DIIS method ilagr lt 0 Zero out gradients along frozen coordinates 0 or 1 Project out gradient components in constrained coordinates Jaguar 6 0 User Manual 187 Chapter 9 The Jaguar Input File 188 Table 9 17 General geometry optimization keywords Continued Keyword Value Description gt 1 Apply constraints using Lagrange multipliers nooptr 0 Optimize all bond lengths not specifically constrained in zmat section 1 Constrain freeze all bond lengths for optimization noopta 0 Optimize all bond angles not specifically constrained in zmat section 1 Constrain freeze all bond angles for optimization nooptt 0 Optimize all torsional angles not specifically constrained in zmat sec tion 1 Constrain freeze all torsional angles for optimization ip472 0 Do not save intermediate structures in the mae output file 2 Save intermediate structures in the mae output file Table 9 18 Keywords for transition state optimizations Keyword Value Description iqst 0 Perform standard non QST transition state search 1 Use quadratic synchronous transit QST methods to guide transition state search Sets itrvec to 5 qstinit 0 5 Distance of LST transition state initial guess between reactant and prod uct geometries Range is 0 0 to 1 0 ifollow 0 For each optimization iteration select a new eigenvector to follow 1 For each optimization iteration follow eigenvector that most closely correlates with one follow
156. ERE A RM MM MM Pa 21 2 6 1 Toolbar Buttons oie eruere Poet bp xe Fed sop ERO NEUE deb IU SEXE NER cub ee 21 2 6 2 PICKING TOO Sii irap ee pM Midi an 22 2 6 3 The Atom Selection Dialog Box uessnnsnnesnnnnnnnnnennnnnnennennnonnnnnnnnnnnnnnnn nenn 23 2 7 Scripting in Maestf u u a a 23 ree e 23 2 7 2 Command SCPI S eae a inet en Sainte ee ieee eae ee eee 24 27 9 Macro S tociens a iacatadec seiieiaiads eiui Md i e Mie 25 Jaguar 6 0 User Manual Contents 2 8 Specifying a Maestro Working Directory ss sss 25 2 9 Undoing an Operation sssssssssseeneeneeenenne nennen 26 2 10 Running and Monitoring Jobs ssse 26 2 11 Getting Help ooa ibd true pin S du pa PEE 28 2 12 Ending a Maestro Session sss 28 Chapter 3 Running Jaguar From Maestro 29 3 1 Sample Calculation sssssssssssseeeeeeeeneeneenenne nenne nennen 29 3 2 The Jaguar Panel 3 3 pied Ei 32 3 3 The Edit Job Dialog BOX sssssssssssessseennennenetntn nennen 34 3 4 Molecular Structure Input nennen 3 4 1 Cartesian Format for Geometry Input 3 4 2 Variables in Cartesian Input 3 4 3 Constraining Cartesian Coordinates orssresnnnennnenennnnnnnnnn nennen nennen 3 4 4 Z Matrix Format for Geometry Input essere 37 3 4 5 Variables and Dum
157. Edit Reset Close Help Figure 4 3 The Theory folder showing LMP2 controls Correlation of orbitals on atom pairs in a virtual space that is restricted to those atoms is not the optimal choice when the orbitals are delocalized as they are in aromatic systems such as benzene Such delocalized orbitals are represented in valence bond theory by resonance struc tures To handle aromatic systems you can delocalize the LMP2 pairs over neighboring atoms in the ring partial delocalization or over the whole ring full delocalization These options are available from the Resonance menu This feature is only available for aromatic rings of 6 or fewer atoms 40 Keyword ireson 1 in the gen section 41 Keyword ireson 2 in the gen section Jaguar 6 0 User Manual 65 Chapter 4 Options 66 Jaguar jaguar l 7 Heiki Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Level of theory GVB GVB 1 GVB Pairs All atom pairs w Hetero atom pairs Start Read Write Edit Reset Close Help Figure 4 4 The Theory folder showing GVB controls 4 6 Generalized Valence Bond GVB Settings The GVB option of the Level of theory option menu allows you to request a Generalized Valence Bond Perfect Pairing GVB PP 20 calculation and to set the GVB pairs for that calculation The theory behind GVB calculations is explained in
158. Exi ge EA M eh a e aL AR 63 4 6 Generalized Valence Bond GVB Settings sss 66 4 7 GVB EMP2 Setliligs jist n reed hier ndr epe iR RUIN AA 67 4 8 SCF SUNOS i i ptg PRU Ma Murus dac AA sek Decus 68 4 8 1 AAcaulacy OVI cauaa cni nes FADE ERRAT asthe NDA M Rear Rar A 68 4 8 2 Convergence Ortena ics st aero e treat ta SP re PA ER denies eee ERR DN eR r EES 69 4 8 3 Convergence Metliods 2 1 tete ee tice een 70 4 8 4 Orbital Treatment uii ioter cou E Poe EIS CERE PEE EEARU IRRSE EAE SEA EXE NICE ERA TA 4 9 Solvation Setlihds oeil ela ois uu Lade t ut adeunt 71 4 10 Properties iim pote te Ge EHE CERTE HERE eee 74 4 10 1 Charges from Electrostatic Potential Fitting 74 4 10 2 Mulliken Population Analysis 5 1 erecti a 76 4 10 3 Multipole Mom6his 52 5 citas iaceo nn 76 4 10 4 Natural Bond Orbital NBO Analysis seeeeeeeeeeeeeeneeenneeeenee Xf 4 10 5 Polarizability and Hyperpolarizability sees Yr 4 10 6 NMR Shielding Constante cs eara pra a VA REERR A FAR en 77 4 11 Frequencies and Related Properties sse 79 4 11 1 Freglendies xin 2 EEE 79 4 11 2 Atomie Masses REM 79 4 11 3 SCaling Of Freduerncies uiii interi tete fa tet echa Y anne 80 4 171 4 Animatiomof Frequenties se ADEM Md EN pu PE 82 Jaguar 6 0 User Manual Contents vi 4 11 5 Infrared Intensities an 83 4 11 6 Thermochemical
159. G KT kl N basis Kw uv uv Qr Kv y Cake j N basis N basis Bi b3 CiyC jy 3 Coy Ci CK JT ij kl and the quantities a and b obey the following rules uu 0 apy 0 byy CyCy for u and v in the same pair u z v and 9 10a 10b 10c 11a 11b Jaguar 6 0 User Manual 159 Chapter 8 Theory 160 2 22 29 ayy 2C C Buy C C 11c for u and v in different pairs Examining the variation of the energy E with respect to the basis set coefficients c gives the equations for the Fock operator corresponding to each GVB natural orbital M 2 gt v v Fy Cyhj 2 Cuvi t byyK 12 v Each orbital s Fock operator thus depends on the other orbitals Coulomb and exchange opera tors At the beginning of each SCF iteration the scf program is provided with a set of proposed natural orbitals and a set of CI coefficients that dictate the contribution of each natural orbital to the GVB orbitals For that set of GVB natural orbitals the program first solves for revised CI coefficients by evaluating the Coulomb and exchange matrix elements for those orbitals and diagonalizing the two by two matrices Y in the basis of the two natural orbitals in pair p as described by these equations Yee Co 13a N 1 vb 2 P Ypg pg Mpg pg 2 ps pet gt Cas 24 ag pg Kag pg 13b q p N vb 2 i Y Cau 27 qu pg Kqu pg q p N 1 vb 2 P Ypu pu 7 h pu pu 27 pu pu
160. GVB wave functions MP2 calcula tions do not generate natural orbitals that could be used for generating surfaces Table 9 41 Keywords for generating plot data Keyword Value Meaning iplotden 0 Do not generate electron density data 1 Generate electron density data iplotspn 0 Do not generate electron spin density data Jaguar 6 0 User Manual Generate electron spin density data Chapter 9 The Jaguar Input File Table 9 41 Keywords for generating plot data Continued Keyword Value Meaning iplotesp 0 Do not generate electrostatic potential data 1 Generate electrostatic potential data iorbla 3 Generate electrostatic potential data 2 Generate electron density data 1 Generate data for all alpha orbitals 0 Do not generate any alpha orbital data gt 0 Index of first alpha orbital for which to generate data iorb2a gt 0 Index of last alpha orbital for which to generate data Ignored unless iorbla is positive iorblb 1 Generate data for all beta orbitals 0 Do not generate any beta orbital data 20 Index of first beta orbital for which to generate data Ignored for restricted wave functions iorb2b 20 Index of last beta orbital for which to generate data Ignored unless iorb1b is positive plotres 2 5 Number of points per unit length The length units are defined by the iunit keyword The default given here is in points bohr xmaxadj 0 0 Amount to adjust the box boundary on the x axis Can
161. H amp The values taken by a variable are defined in a zvar section Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans To specify the values that a variable will take in a scan you can assign a list of values to the variable in the format at number list or you can assign the initial value specified by either number or rom number and two specifications from the following list in the order given in the list e tonumber specify the final value of the coordinate by number specify the step size in integer specify the number of steps Here integer means an appropriate integer and number means an appropriate real number If you specify the initial and final values they are always among the values set For example varying a coordinate from 0 to 120 by a step size of 30 takes 5 steps 0 30 60 90 and 120 As an example to vary the angle HCCH over the values 0 30 60 90 120 150 180 you could use any one of the following lines HCCH from 0 to 180 by 30 HCCH 0 to 180 in 7 HCCH from 0 by 30 in 7 You can also set a coordinate to a set of specific values using the word at With this format the values of the scanned coordinate do not have to be evenly spaced For example this line would vary the angle HCCH over the values 0 30 60 70 80 90 120 150 HCCH at 0 30 60 70 80 90 120 150 You can define up to five scan coordinates at once The first scan coordinate will be in the innermost lo
162. Jaguar 6 0 User Manual O Schr dinger Press Copyright 2005 Schr dinger LLC All rights reserved Schr dinger FirstDiscovery Glide Impact Jaguar Liaison LigPrep Maestro Phase Prime QikProp QikFit QikSim QSite and Strike are trademarks of Schr dinger LLC MacroModel is a registered trade mark of Schr dinger LLC The NCSA HDF5 Hierarchical Data Format 5 Software Library and Utilities is a copyrighted work 1998 2004 of the Board of Trustees of the University of Illinois All rights reserved See the Copyright Notices for full coypright details To the maximum extent permitted by applicable law this publication is provided as is without warranty of any kind This publication may contain trademarks of other companies Please note that any third party programs Third Party Programs or third party Web sites Linked Sites referred to in this document may be subject to third party license agreements and fees Schr dinger LLC and its affiliates have no responsibility or liability directly or indirectly for the Third Party Programs or for the Linked Sites or for any damage or loss alleged to be caused by or in connec tion with use of or reliance thereon Any warranties that we make regarding our own products and services do not apply to the Third Party Programs or Linked Sites or to the interaction between or interoperability of our products and services and the Third Party Programs Referrals an
163. Jaguar 6 0 User Manual 225 Chapter 9 The Jaguar Input File 226 amp gen mp2 3 idelocv 2 amp amp lmp2 C2 C3 C1 C4 amp For QST guided transition state searches with LMP2 wave functions LMP2 delocalization will automatically be performed over neighboring atoms for any bonds present in one structure and not in another unless the input file contains the gen section keyword setting idelocv 0 9 8 The atomic Section The atomic section allows you to specify data for different atoms in a molecule This data can include basis sets for each individual atom or atomic masses a feature that allows isotope calculations You can also use the atomic section to define groups of atoms called fragments where each fragment can then be converted to dummy atoms or counterpoise atoms or used to define a part of the system for which you want to compute a numerical Hessian Restart files may include atomic sections as well in order to keep information about charge fitting or other properties calculated previously In addition atomic sections can be used to supply information about transition metal containing systems that is used to generate high quality initial guesses for these systems See Section 7 1 3 on page 147 for more information on using atomic sections in this manner 9 8 1 General Format of the atomic Section After the amp atomic or atomic line the atomic section should list sets of atomic input values Each of th
164. LIST HOST hostname The string must be unique to ensure that the desired executables are selected The jaguar run command has several other command line options as shown in Table 11 4 For example jaguar run NICE SAVE jobname causes executables to be run with a lower CPU scheduling priority see man page on nice and leaves all temporary files generated during the job in the temporary directory To submit a series of independent jobs you can replace jobname with a list of input file names If you do not specify a host or specify a single host the jobs run sequentially If you specify multiple hosts with the HOST option the jobs are distributed over the hosts specified When a host finishes running a job it starts the next job until there are no more jobs to be run The list of hosts must be separated by spaces and enclosed in quotes For hosts that have more than one processor you can append the number of processors to use to the host name separated by a colon as in the following example jaguar run HOST beta 2 ch4 nh3 You can also use jaguar batch to run multiple jobs If you want to provide Maestro files as input you must use jaguar batch you cannot use jaguar run See Section 11 3 on page 282 for more information Jaguar 6 0 User Manual 277 Chapter 11 Running Jobs 278 11 2 4 Killing a Jaguar Job The jaguar kill command lets you kill any Jaguar job you are running on any host When you use the jaguar ki
165. MESS input file gamess To write out an input file for the program GAMESS you can select this option The resultant file s suffix will be gamess The file will include the molecular geometry the basis set and some information on the type of calculation to be performed as well as the molecular charge and the spin multiplicity of the molecule and any relevant effective core potential information SPARTAN archive file arc You can use this option to generate a SPARTAN 4 0 archive file with the suffix arc XYZ file xyz If you set this option Jaguar creates a file in XYZ format with the suffix xyz The file contains all geometries generated during the course of the job except that for solvated geom etry optimizations the file only contains the solvated structures 6 6 Output Options for Orbitals Orbital information can be printed to the output file as well Several possible choices are avail able in the Orbital Coefficients section of the Output folder If you choose to print out orbital information the output from the program pre lists the non default options chosen above the molecular geometry output from pre and indicates the keywords referred to in footnotes throughout this section You can select options that determine the point at which orbitals are printed out from the Calculation Stage list To select multiple items you can use the SHIFT and CTRL keys in combination with clicks The available items are
166. Molden 83 Witlal Tat Oss M anne 212 virtual orbitals keyword for number printed 216 number printed sess 114 140 W working directory eee 283 Workspace desCrIDtlOTn cioe eei oe aeneo anna he 4 including excluding and fixing entries 15 mouse functions usesenneseenennnennennennnnnn 10 Scratcli entries iiiter 12 X XYZ file xyz output option 139 Z Zero point energies 83 84 130 200 Z matrix format 37 40 170 172 dummy atoms in uuesssessesesnennenennennnnnnnnnn 39 variables in 39 40 171 172 Keyword Index Numerics Plo m 228 B babel eene ECT 209 212 babelg u nennen 209 212 DAS OSS sn aceto ER ETUR 239 basis icone e 200 201 233 C cfiterr esce tentes 196 198 dconvci denspc epsout D o enoro ansias 233 G gcliaree ie eine eis 198 220 259 DIDI 220 259 gconv1 gconv7 osese 191 gdftcphf gdftder2 gdftgrad gdftmed tj rl 220 259 porad 220 259 ICATIOTD een ith cr rena 205 Icavity ooi rre ROS 195 Ul m 196 Ichange 545 0 iii 204 i 185 inn mP 202 MOPEDS P M 233 idelfrag 2 u 0 u en amoena 233 IdeloGy ciet airo ers 179 Idenavg nennen 184 204 POE STN e
167. None CTRL X Exclude selected entries Entry gt Exclude CTRL Z Undo Redo last command Edit gt Undo Redo in main window Jaguar 6 0 User Manual 17 Chapter 2 Introduction to Maestro 18 2 5 Building a Structure After you start Maestro the first task is usually to create or import a structure You can open existing Maestro projects or import structures from other sources to obtain a structure or you can build your own To open the Build panel do one of the following Click the Open Close Build panel button in the toolbar Fa Choose Build from the Edit menu Press CTRL B The Build panel allows you to create structures by drawing or placing atoms or fragments in the Workspace and connecting them into a larger structure to adjust atom positions and bond orders and to change atom properties This panel contains a toolbar and three folders 2 5 1 Placing and Connecting Fragments The Build panel provides several tools for creating structures in the Workspace You can place and connect fragments or you can draw a structure freehand To place a fragment in the Workspace m Select Place 2 Choose a fragment library from the Fragments menu 3 Click a fragment 4 Click in the Workspace where you want the fragment to be placed To connect fragments in the Workspace do one of the following Place another fragment and connect them using the Connect amp Fuse panel which you open from the Edit menu
168. None 1 Job GVB LMP2 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 6 1 The Output folder ables used e g real 8 are listed The total and index i o for the J and K matrices in Mwords are also provided after the energy output from the SCF iterations Detailed timing information If you select this option the CPU time in seconds spent in various Jaguar programs is listed in the output 3 Keyword ip6 2 in the gen section 136 Jaguar 6 0 User Manual Chapter 6 Output Geometries in atomic units also This option allows you to print the geometry output in atomic units as well as in the default units angstroms Multipole moments in atomic units also If you choose to calculate multipole moments by making the appropriate setting in the Proper ties folder this option allows you to list them in the output file in atomic units as well as in the default units debye Bond lengths and angles When this option is turned on the internuclear distances in angstroms are listed for all nearest neighbor atoms in the output from the program pre and the bond angles in degrees are given as well The atoms are indicated with the atom labels assigned in the geometry input When you optimize a geometry this option is turned on automatically For geometry optimizations bond lengths and angles are also listed with the output from the program geopt Connectiv
169. OOU ore 172 174 echo seie A T 239 etields casn eeestis 237 OM E M RT 174 220 QUESS M 235 236 rl 224 225 or n 237 238 lio p 234 235 Imp2 178 225 226 am C 241 242 OIDMAN har rris 238 239 Path uses 239 241 POMC 5 aie een 236 237 zmat zmat2 zmat3 suss 170 171 Za cane ie LARES T 170 zvar Zvar2 zvar eeeeeeeeeeeeeennenennennnnnn 171 172 input of molecular structure see geometry input installation directory 269 289 290 integrals one electron sess 111 integrals two electron contributions to Energy 116 pseudospectral approximation to 157 interface behavior of Maestro 3 internal coordinates in optimization keyword for 187 specifying with connect section 172 174 specifying with coord section 172 174 internal energy calculations 83 84 130 200 intrinsic reaction coordinate IRC calculations sese 102 192 IR intensities see infrared intensities ira program otros enses bi 240 irb program 240 IRC folder nenn 103 isotopes keyword atomic section 228 keyword gen section sess 175 Jaguar 6 0 User Manual 353 Index 354 iterations maximum number geometry optimization 89 149
170. Off zi Molecular state v Use charge and multiplicity from Project Table Create Properties Use these values Molecular charge 0 Spin multiplicity 281 1 pKa atom Use this atom N1 F Pick wv Use pKa atoms from the Project Table Job pKa Start Read Write Edit Reset Close Help Figure 14 1 The Molecule folder for pK calculations The pK atom should be the acidic hydrogen atom in an acid or the basic atom in a base You should also ensure that the structure is in the protonated form for calculations on an acid and in the unprotonated form for calculations on a base If you submit a calculation with the conju gate acid such as an ammonium ion or the conjugate base such as a carboxylate for the input structure the calculation will fail You can submit a pK job for multiple molecules by choosing an option from the Use struc tures from option menu and including or selecting the target molecules or reading the input files For the last option the input files must already include the pK atom designation If you want to run pK calculations for each site in a single molecule that has multiple protona tion or deprotonation sites you can duplicate the entries select Duplicate from the Entry menu Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module in the Project Table panel designate the pK atom for each entry and submit a job with the original and duplicated entries as inp
171. Propenies ia ss 83 4 12 SUMACCS u 24 anes nennen dna Sram amet didt safe 84 Chapter 5 Optimizations and Seas anne ne 87 5 1 Geometry Optimization The Basics sss 87 5 1 1 SCF and Geometry Convergence iiiter tiit baee t cle ute ta EE AES a edd 88 5 1 2 The Initial HESSIAN iiss scat ennena anna ideoida 89 51 3 Coordinate Systems een 90 5 2 Constraining Coordinates sse 90 5 2 1 Freezing Specific COOIdInalBS nungen 91 5 2 2 Applying Constraints by Using Variables seseeeeeene 92 5 2 3 Applying Dynamic Coristralnts ice ehe reati itp dba r ndis cer tit eatis tret apes edge 92 5 3 Transition State Optimizations sssssssseeneeeneee 93 5 3 1 Transition State Search Method reinsert ris et tete ettet zl 93 5 3 2 Specifying Structures for the Reaction csias rancana naine aaae 95 5 3 3 Searching Along a Particular Hessian Eigenvector uessssss 96 5 3 4 Refinement of the Initial Hessian eese 97 5 4 Geometry SCAMS unless dici lump ud ladsbaves 98 5 4 1 Setting up Scans in Maeslio oic ifr hdi ie ree ie pra dug 99 542 Seting up Input Files for Scans s een een 100 5 4 3 RESNO S6aliSoascae EF HHAEUIBR E EE E AT ap PUB ED pane uen Arq EM MES 101 5 4 4 Scan Bies lls 5 9 i ttti te bep id een 101 5 5 Intrinsic Reaction Coordinate Calculations
172. R Goddard W A III Ringnalda M N Won Y Friesner R A Pseudospectral generalized valence bond calculations Appli cation to methylene ethylene and silylene J Chem Phys 1990 92 7488 Ringnalda M N Belhadj M Friesner R A Pseudospectral Hartree Fock theory Applications and algorithmic improvements J Chem Phys 1990 95 3397 Won Y Lee J G Ringnalda M N Friesner R A Pseudospectral Hartree Fock gradient calculations J Chem Phys 1991 94 8152 Friesner R A New Methods for Electronic Structure Calculations on Large Molecules Ann Rev Phys Chem 1991 42 341 Pollard W T Friesner R A Efficient Fock matrix diagonalization by a Krylov space method J Chem Phys 1993 99 6742 Muller R P Langlois J M Ringnalda M N Friesner R A Goddard W A III A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions J Chem Phys 1994 100 1226 Jaguar 6 0 User Manual 335 References 336 12 13 14 15 16 17 18 19 20 2 22 23 Murphy R B Friesner R A Ringnalda M N Goddard W A III Pseudospectral Contracted Configuration Interaction From a Generalized Valence Bond Reference J Chem Phys 1994 101 2986 Greeley B H Russo T V Mainz D T Friesner R A Langlois J M Goddard W A IH Donnelly R E Jr Ringnalda M N New Pseudosp
173. RMPOOL eeereerreeerteteteenees 305 MPT BASSPORT uses 301 304 MPI_USEPASSPORT 301 304 DATH M 290 299 303 REMOTE_JAGUAR_EXEC 303 REMOTE MMSHARE EXEC 303 SCHRODINGER eee 3 4 290 303 SCHRODINGER MPI FLAGS 303 306 SCHRODINGER MPI START 302 SCHRODINGER NODEFILE 301 303 SCHRODINGER POE FLAGS 306 SCHRODINGER TMPDIR 272 ePlayetaincomcoti d utm HERE e 13 14 error messages can t open display 291 child process exited 304 command not found 290 291 loading shared libraries 303 login incorrect eene 294 memory related eese 295 permission denied 293 temp directory eere eto 292 unknown service eee 292 ESP see electrostatic potential exchange corrections in pseudospectral calculations aueh aterert teat 259 exchange operator K keyword for per iteration output 216 keywords for calculation 203 obtaining i o information for 136 pseudospectral assembly of 156 157 excited state calculations using CIS keywords i 185 Up MM 63 excluded entries eiecti 15 executable directory 110 275 selecting with jaguar run 271 execution hosts defimtiomuc en et
174. SIAN input GENET ON isse eann A eee Rr aee Rt troubleshooting SYDLG piorra nee GVB LMP2 calculations ssss 67 H Hamiltonians information in output 113 116 117 user input of sse 237 238 harmonic frequencies see 130 Hartree Fock HF calculations DIIS error vector definition 143 keywords for SCF settings output from standard printing orbitals sss SeltIn S FOR ss elec detrimenti eesi use for GVB initial guess heat capacity calculations Help panel eere Hessian coordinates for refinement of 40 98 effect of quality on geometry CONVELZENCE aeree tte ied eet 89 97 input file section ss 234 235 IRC calculations u 102 194 keywords nter 189 190 Index level shifting rs 189 190 refinement of initial 40 41 97 98 171 172 189 selecting initial 89 90 189 updating keyword for 189 heteroatom pairs GVB calculations ss 66 177 local LMP2 calculations 64 65 178 213 hfigprOBLam xaenocsie o detecte ne 230 OuUtp t PROMI eicere rtg 111 hybrid methods DFT sess 60 hybridization types describing in Lewis files 262 hyperpolari
175. Section 11 2 of the Maestro User Manual for details 2 9 Undoing an Operation To undo a single operation click the Undo button in the toolbar choose Undo from the Edit menu or press CTRL Z The word Undo in the menu is followed by text that describes the operation to undo Not all operations can be undone for example global rotations and transla tions are not undoable operations For such operations you can use the Save view and Restore view buttons in the toolbar which save and restore a molecular orientation 2 10 Running and Monitoring Jobs While Jaguar jobs can be run from the command line we suggest using Maestro to set up and launch these jobs at least until you have some experience with the programs and understand the directory structure and the input file requirements Maestro has dedicated panels for each product for preparing and submitting jobs To use these panels choose the appropriate product and task from the Applications menu and its submenus Set the appropriate options in the panel then click Start to open the Start dialog box and set options for running the job For a complete description of the Start dialog box associated with your computational program see your product s User Manual When you are finished setting the options click Start to launch the job and open the Monitor panel Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Monitor monitor Bl Ii xi Monitoring job benzene Job benz
176. The variable to set depends on how your machine has been configured specifically whether you are running the Job Manager or not The Job Manager manages pools of nodes and assigns specific parallel jobs to specific nodes To test whether you are using the Job Manager type ps aux grep jmd If you see jmd processes listed you are running the Job Manager In this case you need to tell Job Manager the pool from which you want to have nodes assigned to you The command jm status P lists the available pools and their member nodes The environment variable that sets your job pool is called MP RMPOOL and it should be set to the appropriate pool number csh tcsh setenv MP RMPOOL 1 sh ksh bash export MP RMPOOL 1 If your machine does not use the Job Manager you can set the environment variable MP HOSTFILE to the file that contains the host list If MP HOSTFILE is not set then the host file is assumed to be called host 1list and to reside in the current directory see the poe man page The host file should contain the names of the nodes on which parallel jobs can be run The node name is listed once for each processor in that node For example if you have a work station called bobcat with four processors and you want to be able to use all four processors the host file should contain the following four lines bobcat bobcat bobcat bobcat If you call this host file my host file then you should set MP HOSTFILE as follows cs
177. The host name is followed by the number of available processors in parentheses If the host you choose has more than one processor you can run Jaguar in parallel on that host You can enter the number of processors to use in the CPUs text box The default is one processor Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Note You can distribute batch jobs over multiple processors only if you are using the default batch script or the current settings for the batch script The exception is pK jobs which can be run on two processors because they consist of two independent jobs You cannot run MPI parallel jobs as batch jobs The Scratch directory option menu displays a list of directories on the execution host that can be used to store temporary files A subdirectory with the given job name h2o for example is created within the temporary directory and the files from the calculation are stored in this subdirectory If the subdirectory and directory do not have sufficient disk space for the job the job fails If the temporary directory does not exist you should create it or choose a directory which already exists If none of the temporary directory choices already exist and you do not want to create the necessary directories you can change the schrodinger hosts file so that the option menu offers you different choices see Section 11 1 on page 269 3 9 3 Starting and Monitoring Jobs When you are satisfied with the set
178. The nfsh values are zero based pointers to the basis function list The column labeled z lists the exponents for the primitive Gaussians while the coef column lists the coefficient of their contribution to the linear combination comprising the basis func tion Note that the uncontracted basis functions those with jcont values of 1 have coef values of exactly 1 Finally the product of the coef value and the normalization constant for the primitive Gaussian shell N is listed in the column labeled rcoef Gaussian Functions Shell information S j h n e o S f 1 n h S atom 1 t T I h Zz coef rcoef Oo 1 6 0 1 0 5484 6716600 0 0018311 0 8317237 Oo 2 1 0 1 0 825 2349460 0 0139502 1 5308156 Oo 3 1 0 1 0 188 0469580 0 0684451 2 4771485 Oo 4 1 0 1 0 52 9645000 0 2327143 3 2562811 Oo 5 1 0 1 0 16 8975704 0 4701929 2 7928934 O 6 1 0 1 0 5 7996353 0 3585209 0 9549377 Oo 7 3 3T 1 15 5396162 0 1107775 0 6179340 Oo 8 7 3 1 1 3 5999336 0 1480263 0 2757209 O 9 7 3 1 1 1 0137618 1 1307670 0 8142076 O 10 3 1 2 2 15 5396162 0 0708743 3 1169443 Oo 11 10 1 2 2 3 5999336 0 3397528 2 4014375 O 12 10 1 2 2 1 0137618 0 7271586 1 0543604 Oo 13 1 1 1 5 0 2700058 1 0000000 0 2669562 O 14 1 1 2 6 0 2700058 1 0000000 0 2774320 O T5 T 073 9 0 8000000 1 0000000 1 1138249 H1 1 3 0 1 15 18 7311370 0 0334946 0 2149354 H1 2 1 0 1 15 2 8253944 0 2347270 0 3645712 H1 3 1 0 1 15 0 6401217 0 8137573 0 4150514 H1 4 1 0
179. To overcome this problem the parameters for ions are fitted directly to experimental pK data If the gas phase quantum chemistry and neutral solvation are reliably computed then the solva tion free energy of the ionic species becomes the remaining unknown quantity Since pK measurements are carried out to quite high precision in contrast to direct measurements of ionic solvation fitting to this data does not lead to the large uncertainties that would be associ ated with the ionic solvation data Additionally there is an exceptionally large database of known pK values for a wide range of chemical functional groups Jaguar 6 0 User Manual 311 Chapter 14 The pK Prediction Module 312 In general the dielectric radii of ions particularly negative ions are expected to be smaller than that for the corresponding neutral species due to the phenomenon of electrostriction In our fitting procedure the ionic radii are adjusted to yield the smoothest and most consistent results for the members of the training set for each functional group For anions special radii are assigned to the principal location of the negative charge for cations radii are assigned to hydrogens on the proton acceptor and to the proton acceptor itself Functional groups for which radii have been developed are listed in Table 14 1 on page 316 For novel functional groups with divergent electronic properties reparameterization of the model to a subset of experime
180. To run J2 theory calculations select J2 from the Jaguar submenu of the Applications menu The Jaguar panel has only the Molecule and SCF folders because all other input is predefined When you have selected the structures and made any settings click Start You can also use the jaguar j2 command to run the calculation from the command line jaguar j2 options input files This command executes jaguar batch You can run the calculation on a remote host or in parallel by specifying the relevant command options See Section 11 3 on page 282 for details on jaguar batch commands including command line options Jaguar 6 0 User Manual Chapter 4 Options Jaguar provides a wide range of options for performing different kinds of calculations for controlling the convergence of calculations and for controlling the output of calculations Most of these options can be set in the various folders of the Jaguar panel The options that are common to nearly all calculations are set in the following six folders Molecule charge spin symmetry basis set e Theory HF DFT LMP2 GVB GVB LMP 2 CIS restricted unrestricted SCF SCF SCF convergence Properties frequencies surfaces ESP charges Mulliken populations NBO analysis multipole moments polarizabilities Solvation solvent reference energy Output printout options output files The remaining folders that can appear in the Jaguar panel vary according to the task Opt
181. a Jaguar job on the local host hostname submit a Jaguar job to the specified batch queue Replaces h USER Specify the user name to be used for Use the same user name as on the job username remote jobs Must be used with HOST submission host WAIT Wait for the Jaguar job to finish before Return to the command prompt immedi returning to the command prompt ately Replaces w SAVE Save temporary files and temp directory Temporary files are cleaned out of temp for job at end of job Replaces s directory and temporary directory is removed at end of job PROCS Use nprocs processors fora parallel job Run a serial job nprocs Replaces p NICE Run Jaguar executables with nice 19 Jaguar executables are run without nice Replaces n FORCE Force the scratch directory to be over Abort the job if a scratch directory written if it exists Replaces F named for the job already exists t Write time stamps to the log file after Write time stamps to the log file at the each executable has run start and the end of a job DEBUG Print debug information in the terminal Do not print debug information window This information is useful if you need to contact technical support three options are common to all Schr dinger programs You can also use the version options listed in Table 11 3 Note The single letter options h and v are no longer supported The options F n p s and w are still supported but we cannot guarantee that
182. a local MP2 calculation the output from the programs pre and hfig is some what different from that of a Hartree Fock calculation since the use of symmetry is turned off automatically for LMP2 calculations The output from the program scf includes the Coulomb and exchange contributions to the two electron terms for these calculations and the symmetry labels are not included in the output of orbital energies The program loclmp2 which computes localized orbitals runs after scf in an LMP2 calcula tion and its output notes the number of orbitals that are localized Below that output the output from the program 1mp2 appears For local MP2 calculations the output begins by listing the localized orbitals involved in the local MP2 treatment namely the localized orbitals centered on one or both atoms in the pairs of atoms for which an LMP2 level treatment was requested All LMP2 output includes a description of the type of orbitals used in the MP2 calculation First it lists the total number of orbitals Next it lists the number of frozen core and valence MP2 orbitals The numbers of core and valence orbitals will be affected by whether you use valence electrons only or all electrons for the atoms in the calculation Next the numbers of occupied and virtual orbitals for the molecule are listed The list ends with the number of exchange Hamiltonians Some information on the convergence of the LMP2 energy correction appears below the list of orb
183. abel all atoms Jaguar 6 0 User Manual 9 Chapter 2 Introduction to Maestro 10 Display H bonds Choose bond type intra displays H bonds within the selected molecule inter displays H bonds between the selected molecule and all other atoms Delete H bonds Click to select molecule 2 3 3 Measure distances angles or dihe drals Choose a parameter for displaying mea surements Delete measurements Click to select atoms for measurement Mouse Functions in the Workspace The left mouse button is used for selecting objects You can either click on a single atom or bond or you can drag to select multiple objects The middle and right mouse buttons can be used on their own and in combination with the SHIFT and CTRL keys to perform common operations such as rotating translating centering adjusting and zooming Table 2 1 Mapping of Workspace operations to mouse actions Mouse Button Keyboard Motion Action Left click drag Select Left SHIFT click drag Toggle the selection Middle drag Rotate about X and Y axes Adjust bond angle or dihedral Middle SHIFT drag vertically Rotate about X axis Middle SHIFT drag horizontally Rotate about Y axis Middle CTRL drag horizontally Rotate about Z axis Middle SHIFT CTRL drag horizontally Zoom Right click Spot center on selection Right click and hold Display shortcut menu Right drag Translate in the X Y plane Right SHIFT drag vertically Trans
184. act Liaison and QSite J aguar LigPrep MacroModel Phase Prime QikProp and Strike It contains tools for building displaying and manipulating chemical structures for organizing loading and storing these structures and associated data and for setting up monitoring and visualizing the results of calculations on these structures This chapter provides a brief introduction to Maestro and some of its capabilities For more information on any of the topics in this chapter see the Maestro User Manual 2 1 General Interface Behavior Most Maestro panels are amodal more than one panel can be open at a time and a panel need not be closed for an action to be carried out Each Maestro panel has a Close button so you can hide the panel from view Maestro supports the mouse functions common to many graphical user interfaces The left button is used for selecting choosing menu items clicking buttons and selecting objects by clicking or dragging This button is also used for resizing and moving panels The right button displays a context sensitive menu Other common mouse functions are supported such as using the mouse in combination with the SHIFT or CTRL keys to select a range of items and select or deselect a single item without affecting other items In addition the mouse buttons are used for special functions described later in this chapter These functions assume that you have a three button mouse If you have a two button m
185. active atom again to finish drawing Jaguar 6 0 User Manual 19 Chapter 2 Introduction to Maestro 20 2 5 2 Adjusting Properties In the Atom Properties folder you can change the properties of the atoms in the Workspace For each item on the Property option menu Element Atom Type MacroModel Partial Charge PDB Atom Name Grow Name and Atom Name there is a set of tools you can use to change the atom properties For example the Element tools consist of a periodic table from which you can choose an element and select an atom to change it to an atom of the selected element Similarly the Residue Properties folder provides tools for changing the properties of residues the Residue Number the Residue Name and the Chain Name To adjust bond lengths bond angles dihedral angles and chiralities during or after building a structure use the Adjust distances angles or dihedrals button on the main toolbar You can also open the Adjust panel from this button menu from the Display Adjust panel button on the Build panel toolbar which has the same appearance as the above button or from the Edit menu in the main window 2 5 3 The Build Panel Toolbar The toolbar of the Build panel provides quick access to tools for drawing and modifying struc tures and labeling atoms See Section 2 3 2 on page 7 for a description of the types of toolbar buttons The toolbar buttons and their use are described below in the Workspace pla
186. adings should be read down rather than across For the table of SCF iteration information the number of the iteration is provided first in each row followed by a Y or N indicating whether the Fock matrix was updated or not The Jaguar 6 0 User Manual 0 0 ooo 1 000000 Symmetry A1 000000000000000 000000000000000 003807504316264 000004988565650 000252040203901 000372571507087 1 000000 Symmetry A1 000000000000000 000000000000000 0 148513692384474 013419565122871 022047889711935 008194082815896 1 000000 Symmetry Al 00000 0 00155 0 00430 0 00000 0 00000 0 00019 00000 0 00000 0 00000 0 00000 0 00034 0 00000 00034 0 00000 0 00037 0 00025 1 345597 Occupation 1 000000 Symmetry Al 00000 0 08586 0 41777 0 00000 0 00000 0 03150 00000 0 00000 0 00000 0 14851 0 01307 0 00000 01307 0 00000 0 02205 0 01342 Chapter 6 Output Fock matrix is updated using the difference in density matrix between iterations to accumulate contributions The next entry indicates whether the DIIS convergence scheme was used for that iteration also with a Y or N The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that iteration DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this column reads A it indicates that DIIS was not us
187. adjusts the charge when it uses these structures The same rules apply to the structure as for a single input file if you are doing calculations for an acid both structures must be protonated and if you are doing calculations for a base both structures must be deprotonated So for example if you performed a conformational search with Macro Model on an amine and its corresponding ammonium ion you would have to remove a proton from the ammonium ion structure before putting it in the acidfile in input file The number of processors used for parallel execution is nproc and must be either 1 or 2 If you select two processors the acid and base sections of the job are initiated as separate Jaguar jobs Selecting more processors does not run the separate Jaguar jobs in parallel If you want to run more than one pK job with a single command you must use the jaguar batch command and specify pka bat as the batch file jaguar batch options pka bat jobnamel jobname2 The input files for the pK jobs must be in the format described above Use of the wildcard in job names is allowed You cannot specify separate protonated and deprotonated species with the batch command The command options are described in Table 11 3 Table 11 4 and Table 11 8 14 4 5 Monitoring pK Calculations The pK calculations can be monitored from the Maestro Monitor panel or by looking at the file pka blog where is a process identification number For ea
188. age 196 4 10 6 NMR Shielding Constants Gas phase NMR shielding constants are available for closed shell and unrestricted open shell wave functions To calculate chemical shifts you should calculate NMR shielding constants for the reference molecules for each element of interest in the same basis set and with the same method as for the molecule of interest 75 Empty nbo section in the input file 76 Keyword ipolar 1 and 2 in the gen section 77 Keyword ipolar 1 for alpha or 2 for alpha and beta in the gen section 78 Keyword ipolar 5 in the gen section 79 Keyword ipolar 7 in the gen section 80 Keyword nmr 1 in the gen section Jaguar 6 0 User Manual 77 Chapter 4 Options 78 BEE Jaguar jaguar Use structures from Workspace included entries Molecule Theory scr Properties Solvation Output Properties select to edit options Calculate Vibrational frequencies Surfaces MO density potential Atomic electrostatic potential charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability m Polarizability Hyperpolarizahility Property Method alpha 3 point finite field Finite field 0 0240 atomic units Job B3LVP 6 31G Single Point Energy Start Read Write Edit Reset Close Help Figure 4 8 The Properties folder showing controls for p
189. age 226 which describes the atomic section of the input file if you want information on the other information in this table Jaguar 6 0 User Manual Chapter 6 Output After the pre output the usual output appears for the first gas phase calculation except that the energy breakdown for the sc output also describes the electron nuclear and kinetic contri butions to the total one electron terms in the energy as well as the virial ratio V T where V is the potential energy and T is the kinetic energy This ratio should be 2 if the calculation satis fies the virial theorem After the first sc output the output from the first run of the program ch appears Since performing a solvation calculation enables electrostatic potential fitting to atomic centers the usual output for that option which is described in Section 6 3 7 on page 124 is included every time output from the program ch appears in the output file The post program writes out the necessary input files for the Poisson Boltzmann solver this step is noted in the output file The next output section comes from the Poisson Boltzmann solver The output includes infor mation on the area in of the molecular surface formed from the intersection of spheres with the van der Waals radii centered on the various atoms the reaction field energy in KT where T 298 K which is the energy of the interaction of the atom centered charges with the solvent the solvent accessible s
190. age 262 for more information while the right most digit specifies the number of bonds to elements and hybridization types that do not fit into any of the groups described for the element of the atom being evaluated For example suppose only one hybridization group were described for carbon in the sample Lewis file as follows Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files 6 CARBON Group 1 C C sp3 bonds 1 hybridization Sp3 hybridization 1 atom 6 Then this atom type description line in a Lewis file would accurately match the middle carbon in propylene H C CH CH 6 I SEQ vet c 2 00 C in H2 C C or H2 C O as would the following line which also contains the proper settings for the middle carbon s hybridization and bonding type 6 6 111 12 1 1 2 00 C in H2 C C or H2 C O As for the integer describing bonding type the total of the digits in the fourth integer should be the same as the number of bonds three for this example remembering that the double bond counts as one bond that is all bonds should be accounted for unless of course the integer is 1 The fifth and sixth integers describe the ring the atom is in if any If the fifth integer is a posi tive number n it indicates that the atom description corresponds to an atom in a ring of size n For example a benzene carbon is in a ring of size 6 If the fifth number is a negative number n the description corresponds to an atom in a ring of size
191. al Hessian to be used for the optimi zation To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the zvar section line that defines the variables For instance a job that included Hessian refinement that was run with the following zmat section would use both O H bonds and the H O H angle in the refinement amp zmat O1 H2 gl T1 1 H3 O1 1 1 H2 108 0 amp Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For instance for the water input example shown above only two coordinates will actu ally be refined the O H bond distance which is the same for both bonds and the H O H angle if molecular symmetry is used for the job Certain types of transition state optimizations require that you enter two or three geometries see Section 5 3 on page 93 for details For these jobs you can input the second and third geometries Geometry 2 and Geometry 3 in the zmat2 and zmat3 sections The order of atoms in the input must be the same as in the zmat section Alternatively if the changing coor dinates in the zmat section are set using variables you can leave out the zmat2 and zmat3 sections and specify the second and third geometries by adding zvar2 and zvar3 sections which will be used in combination with the zmat sectio
192. al describing how to set up run and interpret jobs is presented Jaguar 6 0 User Manual 309 Chapter 14 The pK Prediction Module 310 14 1 Theory of pK Calculation 14 1 1 Abinitio Quantum Chemical Calculation of pK Values The calculation of the pK of a molecule in aqueous solution can be represented as a thermody namic cycle A BH 95 Bg Hy p je BH aq gt Bag H ap The strategy in our pK module is to calculate parts A B and C of the above cycle whereupon the actual pK which is related to D by 1 PK yan can be obtained by summing the free energy changes for these three components and the experimental value of 259 5 kcal mol for the solvation free energy change of a proton Segment A is the gas phase reaction A BH 9 5 Bg Hg The gas phase free energy difference between the protonated and deprotonated states can be computed via the usual relations A AH TAS Eg Esme 5 2RT TAS B g Evaluation of this expression requires the following quantum chemical calculations 1 Geometry optimization of the protonated and deprotonated species Quantum chemical methods generally carry out a conjugate gradient optimization and hence cannot search for multiple minima We assume here that there is only a single well defined conforma tional minimum and that a good initial guess obtained for example from molecular mechanics or semiempirical quantum chemistr
193. al method runs next but has no significant output An example of the output from the next program scf again for a water molecule is given here and is explained below start of program scf number of electrons 10 number of alpha electrons 5 number of beta electrons 5 number of orbitals total 25 number of core orbitals 5 number of open shell orbs 0 number of occupied orbitals 5 number of virtual orbitals 20 number of hamiltonians 1 number of shells 1 SCF type HF i u d i g t p i amp RMS maximum e d i u i energy density DIIS r t t d total energy change change error etot 1 N N 5 M 75 61350567257 1 6E 02 3 3E 01 etot 2 Y Y 6 M 75 99456008691 6 2E 03 6 9E 02 etot 3 Y Y 6 M 76 01904109359 1 7E 03 2 9E 02 etot 4 N Y 2 U 76 02333233097 7 6E 04 4 7E 03 etot 5 Y Y 6 M 76 02361760760 1 7E 04 1 5E 03 Jaguar 6 0 User Manual Chapter 6 Output etot 6 Y N 6 M 76 02364072535 2 3E 05 0 0E 00 0 0E 00 Energy components in hartrees A Nuclear repulsion 9 33000672144 E Total one electron terms 123 34165776264 I Total two electron terms 37 98801031585 L Electronic energy 85 35364744679 E I N Total energy 76 02364072535 A L SCFE SCF energy HF 76 02364072535 hartrees iterations 6 HOMO energy 0 49745 LUMO energy 0 21516 Orbital energies symmetry label
194. all and Stick file bef MSI BGF file bmin MacroModel file box DOCK 3 5 box file caccrt Cacao Cartesian file cacint Cacao Internal file cache CAChe MolStruct file c3dl Chem3D Cartesian 1 file c3d2 Chem3D Cartesian 2 file cdct ChemDraw Conn Table file diag DIAGNOTICS file dock Dock Database file wiz Wizard file contmp Conjure Template file Cssr CSD CSSR file dpdb Dock PDB file feat Feature file fhz Fenske Hall ZMatrix file gamin Gamess Input file gcart Gaussian Cartesian file gzmat Gaussian Z matrix file gotmp Gaussian Z matrix tmplt file gr96A GROMOS96 A file gr96N GROMOS96 nm file Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 31 Output format keywords and file types for babel file format conversions Continued Format Keyword File Type hin Hyperchem HIN file icon Icon 8 file idatm IDATM file sdf MDL Isis SDF file jagz Jaguar Z Matrix file jage Jaguar Cartesian file m3d M3D file macmol Mac Molecule file macmod Macromodel file micro Micro World file mm2in MM2 Input file mm2out MN2 Output file mm3 MM3 file mmads MMADS file mdl MDL Molfile file miv Mollnventor file mopert Mopac Cartesian file mopint Mopac Internal file csr MSI Quanta CSR file pemod PC Model file pdb PDB file psz PS GVB Z Matrix file psc PS GVB Cartesian file report Report file smiles SMILES file spar Spartan file mol Sybyl Mol file mol2 Sybyl MoD file Jaguar 6 0 User Manual 211 Chapter 9 Th
195. and p86 for correlation Jaguar 6 0 User Manual 179 Chapter 9 The Jaguar Input File 180 Table 9 8 Standard functional names for the dftname keyword Name Description hfs Slater local exchange functional 29 xalpha Xa local exchange functional 29 hfb Slater local exchange functional 29 Becke 1988 non local gradient correction to exchange 32 hfpw Slater local exchange functional 29 Perdew Wang 1991 GGA II nonlocal exchange 31 bp86 vwn5 Exchange Slater local functional 29 Becke 1988 non local gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Perdew 1986 gradient correction functional 35 pwpw91 Exchange Slater local functional 29 Perdew Wang 1991 gradient correction functional 31 correlation Perdew Wang 1991 GGA II local and nonlocal func tionals 31 hcth407 Hamprecht Cohen Tozer Handy functional including local and nonlocal exchange and correlation reparametrized with a training set of 407 molecules by Boese and Handy 40 pbe Perdew Burke Ernzerhof local and nonlocal exchange and correlation functional 41 b3lyp Exchange exact HF Slater local functional 29 Becke 1988 nonlocal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 Lee Yang Parr local and nonlocal functional 33 b3pw91 Exchange exact HF Slater local functional 29 Becke 1988 non local gradient correction 32 correlation Perdew Wang 1991 l
196. and the backward direction toward the reactants IRC scans have been implemented in Jaguar using the methods described in Ref 149 The implementation includes both IRC and minimum energy path MEP calculations The differ ence between the two is that the reaction coordinate for the IRC path is mass weighted whereas the reaction coordinate for the minimum energy path is not IRC calculations can be set up from Maestro or by adding keywords to an input file see Section 9 5 11 on page 192 To set up an IRC or minimum energy path calculation from Maestro you must first perform a transition state calculation and read in the restart file then choose Reaction Coordinate from the Jaguar submenu of the Applications menu The calculation requires an accurate Hessian for the transition state You can either precalcu late the Hessian and read it in from the restart file or make the calculation of the Hessian part of the IRC or MEP calculation This choice can be made from the Initial Hessian option menu in the Optimization folder to read the Hessian choose Other to calculate the Hessian choose 29 Keyword inhess 2 in the gen section Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans Jaguar jaguar Jl imixi Molecule Theory scr Optimization IRC Properties Solvation Output Direction Forward Reverse Structures Transition state lt j trans_freq 01 Choose Reactant alcohol Choose
197. ans have the same exponents The next number in that line is the polarization diffuse function parameter If it is 1 it indicates a polar ization function which is included in the basis set if the basis set name ends in an as described in Section 4 2 on page 55 If the number is 2 it indicates a basis set function if 1 a basis set function if 2 a basis set function Otherwise the number should be 0 The rest of the numbers on that line determine the way that Jaguar will contract some of the functions and the range of each function The numbers before the dash describe how many of the functions are included in that contraction For example if there were two such numbers 2 and 1 the line would indicate that Jaguar would contract the first two Gaussians provided immediately below into one contracted function and would treat the third Gaussian as an uncontracted function If you want to add or change a basis set to a basis file you should probably contract together all Gaussians whose exponents are greater than 0 3 The default basis information gener ally follows this rule although there are some exceptions see the Li s and p function informa tion in the sample file below for an example The numbers after the dash describe the range of each such function There should be one such number for each contraction number before the dash A zero indicates that the contracted func tion will be treated as a long ra
198. as for the bonding type information The beginning of the hybridization information in a sample 1ewis file illustrating a list of hybridization type information for hydrogen and carbon is shown below with some comments to further explain the file format HYBRIDIZATION TYPE 01 INFORMATION 1 HYDROGEN Group 1 H C sp2 bonds 1 hybridization Sp2 hybridization sp2 hybr MUST have 5 spaces before it 1 element 6 Group 2 H O sp3 bonds 1 hybridization sp3 hybridization 1 element 8 KKK 6 CARBON Group 1 C C sp3 bonds 1 hybridization sp3 hybridization 1 atom 6 Jaguar 6 0 User Manual 263 Chapter 10 Other Jaguar Files 264 The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines and the hybridization labels After all desired hybridization types are described for all appropriate elements the hybridiza tion type information should end with a blank line 10 6 3 Setting van der Waals Radii From Lewis File Data The Lewis file can be used to make non default choices for van der Waals radii of atoms in particular chemical environments or even to reset the default radii for particular elements After Jaguar s lewis program analyzes an input geometry s Lewis dot structure it sets the atom s van der Waals radius to the value dictated by the first atom type description of element and chemical environment in the Lewis file that matches that atom
199. ata may be spread over multiple lines As explained above the beginning of the default grid file indicates that five grid types are listed for each atom corresponding to the coarse medium fine ultrafine and gradient grids All coarse grids for 6 31G with or without the polarization functions indicated by the will set the boundary plane between atoms described earlier at the point where the grid point densities are the same for the two atoms because of the 1 flag Next seven shells apiece are specified for H atomic number 1 He atomic number 2 and Li atomic number 3 The actual default grid file continues with a list of coarse atomic grids for the other atoms in the basis set followed by the medium fine and ultrafine atomic grids in the same format before proceeding to define the grids for another basis set in the same manner The possible values of the numbers on the angular grid line are listed in Table 10 1 along with the corresponding number of points per angular shell and the degree of the highest spherical harmonic which the grid integrates exactly when relevant The full references are provided in a section beginning on page 335 Table 10 1 Number of points per angular shell and degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line Entry Points Degree Reference for Grid 1 6 3 Un 3 1 Stroud p 294 135 3 8 3 Un 3 2 Stroud p 2
200. ation This command gives the same output as the SCHRODINGER machid com mand Report information on the hardware platform This command gives the same output as the SSCHRODINGER platform command List the available batch scripts Report any system requirements for Jaguar and whether they are met Display a command syntax summary including a list of valid commands Jaguar 6 0 User Manual 273 Chapter 11 Running Jobs 274 For example the commands jaguar run h2o jaguar run h2o in both run a Jaguar job with the job name h2o and the input file h2o0 in The job control functions of the jaguar command jobs kill stop and purge are now interfaces to the jobcontrol command with Jaguar selected as the program For instance jaguar jobs actually executes jobcontrol list program jaguar In addition to running the commands listed in Table 11 1 you can use the jaguar command with the options listed in Table 11 2 to obtain information about Jaguar versions and hosts available Some of these options can be qualified by arguments that limit or define the list of versions displayed These version arguments are listed in Table 11 3 To find out about versions available on remote hosts you can add the qualifier HOST hostname For example to check whether version 4 2 of Jaguar is installed on the host reda you could use the following command jaguar WHICH HOST freda REL v42 Further examples are given in
201. b control facility handles scratch directory creation and cleanup and ensures that each job has a unique scratch directory Output files are copied to the working directory while the job is running Detailed information on job control can be found in the Maestro User Manual Some of this information is repeated here If you intend to run jobs on various hosts you must provide information on the hosts to the job control facility through a file named schrodinger hosts How to provide this information is described in the next section In addition to using the job control facility you can use the jaguar command to perform a number of job submission tasks The jaguar command is described in the following section and creating batch scripts to submit multiple Jaguar jobs is described in the subsequent section 11 1 Customizing Host Configurations The installation directory SCHRODINGER contains a file named schrodinger hosts that identifies hosts on which Jaguar can be run and provides some information about the use of the host When you start Maestro the settings in the schrodinger hosts file are used to deter mine the available options in the Start dialog box You can copy and edit the schrodinger hosts file to customize its settings You shouldn t need to update any schrodinger hosts files when you later install other versions of Jaguar Information on the schrodinger hosts file is given in the Schr dinger Product Installation Guide and include
202. b is launched in addition to MPI PASSPORT and MPI USEPASSPORT The value yes requests a single attempt to launch the secure servers An integer value specifies the time limit in seconds for attempts to launch the servers which are made every 10 seconds By default the secure servers are not launched within the job The servers continue to run after the job is finished While serv p4 provides a fast secure method of starting up MPI processes throughout a network it may not be compatible with certain security settings file system configurations or user authentication mechanisms If you believe that serv p4 is incompatible with your computing environment you may be able to avoid using it by setting the environment variables Jaguar 6 0 User Manual Chapter 13 Parallel Jaguar that Jaguar needs in your shell startup scripts In addition to setting SCHRODINGER to the instal lation directory you must set the following environment variables JAGUAR EXEC SSCHRODINGER jaguar vjversion bin Linux x86 MMSHARE EXEC S SCHRODINGER mmshare vmversion bin Linux x86 REMOTE JAGUAR EXEC S SCHRODINGER jaguar vjversion bin Linux x86 REMOTE MMSHARE EXEC S SCHRODINGER mmshare vmversion bin Linux x86 LD LIBRARY PATH S SCHRODINGER jaguar vjversion lib Linux x86 where jversion is the 5 digit Jaguar version number and mversion is the 5 digit mmshare version number You must also ensure that the mpirun s
203. be positive or negative xminadj 0 0 Amount to adjust the box boundary on the x axis Can be positive or negative xadj 0 0 Amount to adjust the x dimension of the box Half the adjustment is added to each boundary Can be positive or negative ymaxadj 0 0 Amount to adjust the box boundary on the y axis Can be positive or negative yminadj 0 0 Amount to adjust the box boundary on the y axis Can be positive or negative yadj 0 0 Amount to adjust the y dimension of the box Half the adjustment is added to each boundary Can be positive or negative zmaxadj 0 0 Amount to adjust the box boundary on the z axis Can be positive or negative zminadj 0 0 Amount to adjust the box boundary on the z axis Can be positive or negative Jaguar 6 0 User Manual 223 Chapter 9 The Jaguar Input File 224 Table 9 41 Keywords for generating plot data Continued Keyword Value Meaning zadj 0 0 Amount to adjust the z dimension of the box Half the adjustment is added to each boundary Can be positive or negative plotfmt vis or Set the format and file extension for plot files to vis the default vis Maestro format plt or Set the format and file extension for plot files to plt plt When the job is run each type of output requested is written to a file whose name depends on jobname the name for the job for example h20 and the type of information being plotted The file name stem is jobname density for a density plot jo
204. bles HTML in its use of tags to enclose sections of ordinary text The tags identify the purpose of the enclosed text For example the pK module informa tion for carboxylic acids looks like this Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module functional group name carboxylic acid jaguar id 4 jaguar fl 0 4451 2 0 2516 gt lt smarts gt 110 CX3 0 lt smarts gt lt smarts gt OX1 CX3 2O lt smarts gt functional group where name is a double quoted string that describes the functional group jaguar id is a unique index number for the functional group and 1 and 2 are the pK correction factors The group numbers are listed in the jres File Group Number column of Table 14 1 The first SMARTS pattern describes the acidic form of the molecule while the second SMARTS pattern describes the basic form of the molecule For more information on SMARTS patterns see the web page http www daylight com dayhtml doc theory theory smarts html The two pK correction factors 1 and 2 come from a linear fit of the calculated pK values to the experimental values for a particular training set of molecules f1 is the slope and 2 is the intercept You can perform linear fits with many commonly available software programs Here are some suggestions for selecting a set of molecules to use as a training set for the devel opment of new pK correction parameters Select molecules for whi
205. bname spin for a spin density plot and jobname potential for a potential plot Orbital plot information is written to sepa rate files for each orbital The orbital file name stems are of the form jobname spin MO g where spin can be alpha or beta and is the orbital index number For instance the fifth orbital from the job h20 would be written to the file h20 alpha MO 5 vis A plt file begins with an echo of the plot section used to generate it The rest of the lines in the plt file contain values of the relevant property to be plotted on the grid first varying the z coordinate then the y coordinate then the x coordinate the loop over z values is the innermost loop The vis file is a binary file Note The plot section is deprecated but is still generated internally and written to the plt file You can still include a plot section in an input file 9 6 The gvb Section The gvb section whose GUI equivalent is described in Section 4 6 on page 66 is not keyword based The section should contain the pair settings in any order unless you are using the Lewis dot structure keywords described in Section 9 5 5 on page 176 Each line describing a bond pair should contain three integers which specify the type of bond 1 for sigma 2 for pi 3 fora second pi in a triple bond and the atom number labels of the two atoms in the GVB pair Each line describing a lone pair should contain a number identifying the lone pair followed by the number
206. bs Table 11 6 Batch input file directives Directive Action EXEC directory OUTDIR directory SCRATCH directory TMPDIR directory WORKDIR directory files FLAGS options OPTIONS options OUTFILES files IGNORE _ ERRORS PURGE JOBDB EXIT Set the directory for the Jaguar executable This directory can be any directory listed by jaguar LIST Set the directory to which output from jobs will be written The default is the job submission directory This directory is created auto matically if it does not exist Set the scratch directory Equivalent to specifying the JAGUAR SCRATCH environment variable Set the scratch directory root Equivalent of tmpdir setting in schrodinger hosts Create the specified directory and use it as the working directory for input and output Copy the specified files into the directory The default is the job submission directory Specify jaguar run command line options Set options to apply to subsequent jobs Options can be specified over multiple lines by using on the first line and on subsequent lines Options are listed in Table 11 7 Copy the specified files from WORKDIR to OUTDIR at the end of the job The file list can be spread over multiple lines by using on the first line and on subsequent lines Continue to the next job if a job step fails The default is to stop exe cution of the batch script and exit Purge the
207. c in the Selected constraint section next to the table and enter the value that you want the constraint to converge on in the Target value text box This value is copied to the Target column of the table and added to the variable definition in the coord section 5 3 Transition State Optimizations To perform transition state searches with Jaguar you can use either a simple quasi Newton method that searches for the transition state nearest to the initial geometry or quadratic synchronous transit QST methods also known as synchronous transit quasi Newton STQN searches We generally recommend using QST methods any time you can provide both reac tant and product geometries To set up a transition state search choose Transition State Search from the Jaguar submenu of the Applications menu in the main window You can set optimization parameters that are not unique to transition state searches in the Optimization folder The Transition state folder contains controls for settings that are specific to transition state searches including selection of the reactant and product geometries This section describes various transition state search options For information on general settings that are useful for all types of geometry optimizations see Section 5 1 on page 87 5 3 1 Transition State Search Method The first choice listed in the Transition State folder is the Search method which can be set to Standard LST or QST The default ch
208. can change bond lengths bond angles dihedral angles or atom chiralities Add hydrogens H Choose an atom type for applying the current hydrogen treatment Same as the Add hydro gens button on the main toolbar see page 8 Geometry Symmetrizer 3 Open the Geometry Symmetrizer panel for symmetrizing the geometry of the structure in the Workspace ae Geometry Cleanup coe Clean up the geometry of the structure in the Workspace 2 6 Selecting Atoms Maestro has a powerful set of tools for selecting atoms in a structure toolbar buttons picking tools in panels and the Atom Selection dialog box These tools allow you to select atoms in two ways Select atoms first and apply an action to them Choose an action first and then select atoms for that action 2 6 1 Toolbar Buttons The small triangle in the lower right corner of a toolbar button indicates that the button contains a menu Many of these buttons allow you to choose an object type for selecting choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit Jaguar 6 0 User Manual 21 Chapter 2 Introduction to Maestro 22 For example to select atoms with the Workspace selection toolbar button 1 2 Choose Residues from the Workspace selection button menu A The button changes to R Click on an atom in a residue in the Workspace to select all the at
209. ce display options in Maestro Orbital surfaces can be generated only for SCF and GVB wave functions MP2 calculations do not generate natural orbitals that could be used for surfaces For GVB wave functions surfaces are generated for the natural orbitals You can generate data for all surfaces in the same run The data for each surface is written to a separate vis file The data for the property volume data is tabulated on a three dimensional rectangular grid The box containing the grid encompasses the van der Waals radii of all atoms in the molecule You can adjust the box size within the range 1 to 25 and you can change the density of grid points within the range 1 25 points A using the Box size adjustment and Grid density text boxes in the Surfaces section The orbital selection controls depend on whether you have an initial guess or not If you do not have an initial guess you can select the orbitals to plot in a range relative to the HOMO and LUMO If you do have an initial guess a list is displayed with the orbital index energy and occupation You can select a range of orbitals from this list with the SHIFT key If the wave function is spin unrestricted you can choose alpha and beta orbitals independently When the job to generate the data finishes the surfaces are imported into Maestro and the first surface is displayed If your molecule is not already an entry in the Project Table the surfaces are not automatically
210. ces an atom and connects it to the previous atom Delete Choose an object for deleting Same as the Delete button on the main toolbar see page 8 Set element Choose an element for changing atoms in the Workspace default C Click an atom to change it to the selected element Free hand drawing va Choose an element for drawing structures freehand in the Workspace default C Each click 4 X C Increment bond order U Select a bond to increase its bond order by one to a maximum of 3 Select a bond to decrease its bond order by one to a minimum of 0 Decrement bond order iC Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Increment formal charge Select an atom to increase its formal charge by one Decrement formal charge Select an atom to decrease its formal charge by one Move Choose a direction for moving atoms then click the atom to be moved Moves in the XY plane are made by clicking the new location Moves in the Z direction are made in 0 5 A increments Label P Apply heteroatom labels as you build a structure The label consists of the element name and formal charge and is applied to atoms other than C and H MM ERE Display Connect amp Fuse panel y amp Open the Connect amp Fuse panel so you can connect structures create bonds between struc tures or fuse structures replace atoms of one structure with those of another Display Adjust panel Open the Adjust panel so you
211. ch molecule Jaguar creates a jobname_pka subdirectory in the local directory and writes the input and output for each job step there The input and output filenames have suffixes appended to jobname that explain what is calculated in each step These suffixes are listed in Table 14 3 Final pK and pK values are calculated from data in these output files and written in jobname out in the local directory where jobname in is a Jaguar input file submitted for a pK calculation For example here is the final output file for formic acid Stoichiometry Charge pK CH202 0 pKa 3 2 CHO2 1 pKb 10 8 To list in a table all the pK and pK values you can use the jaguar results command jaguar results title jobname pka pkb out Jaguar 6 0 User Manual 329 Chapter 14 The pK Prediction Module 330 Table 14 3 File suffixes for pKa calculations Suffix Job Step Explanation dft h B3LYP 6 31G geometry optimization for conjugate acid nrg h B3LYP cc pVTZ f single point energy for conjugate acid solv h B3LYP 6 31G single point solution phase calculation for conjugate acid prt h input file preparation runs for conjugate acid dft B3LYP 6 31G geometry optimization for conjugate base nrg B3LYP cc pVTZ f single point energy for conjugate base solv B3LYP 6 31G single point solution phase calculation for conjugate base prt input file preparation runs for conjugate base 14 4 6 Choice of Initial Geometry
212. ch the experimental pK values are accurately known Aqueous pK values near 14 and beyond or near 0 and beyond are not generally accurate because of the difficulty in measuring the concentration of acid or base in the presence of high concentrations of hydronium or hydroxide the leveling effect All of the experimental pK values must be in the same solvent at the same temperature plus or minus a few degrees pK values in mixed solvents are not a good choice This is because the continuum solvation model used by Jaguar requires the specification of a sin gle solvent dielectric constant and probe radius and it is not known how these parameters should be specified for a mixed solvent system especially when the degree of preferential solvation of the solute is unknown Try to obtain experimental pK values that cover as wide a pK range as possible for the given functional group This ensures that the fitting parameters are broadly applicable to molecules containing that functional group The more molecules you use in the training set the more clearly you can see how well the calculated pK correlates with the experimental pK and the better idea you will have of the RMS error Jaguar 6 0 User Manual 331 Chapter 14 The pK Prediction Module Do not select training set molecules that contain symmetrically equivalent functional groups An additional correction term is required in this case to account for the increased entro
213. change terms for pairs of orbitals i and j Orbitals which have the same a and b coefficients and number of electron pairs f are considered to be in the same shell The first line in the ham section should indicate the number of core orbitals for the molecule Next each shell is described in turn The first line of each shell description should contain two numbers the first an integer indicating the number of orbitals in that shell and the second a real number indicating f the number of electron pairs in each orbital of that shell The next line should contain the a terms for any orbital in the shell where j i and j is not a core orbital The last line describing the shell lists all b terms for any orbital in the shell where j lt i and j is not a core orbital 9 14 The orbman Section The orbman section allows you to reorder orbitals in the guess section of a restart file or to form linear combinations of orbitals The format of the orbman section is as follows amp orbman hfiglcmo i j amp k 1 p end amp where i j k and are integers indicating the ith jth kth and lth orbitals before mixing i e X Xj Xj and Xj and amp and B are angles in degrees indicating the degree of mixing The command hfiglcmo mixes the orbitals to form orbitals X474 7 xp according to the following equations new and x new X 7 X cosa X sina new ci X Xjcoso x sino n jo d x cosB x sinB
214. chemical and pharmaceutical industries are specifically designed to work with the basis sets electron corre lation levels and solvation model of the ab initio methodology The transferability of the corrections has been tested by examining a sizeable set of test molecules Several features of the method distinguish it from purely empirical fragment based approaches which are complementary to the present product First we expect that the use of ab initio quantum chemistry rather than fragment table lookups and interpolation will lead to a substantially wider range of applicability as well as significantly higher precision when the compound in question is not a direct entry in the empirical table Second our methods allow for a reasonable treatment of conformational effects which are in general entirely missing from fragment based methods Optimal use of the methodology in this fashion is accomplished by performing solution phase conformational searches with MacroModel Third the method can handle multiple protonation states in a systematic fashion This chapter is divided into four sections First the basic theory of pK calculations is explained including a discussion of the empirical correction approach Then a discussion of key issues in using the program in complex situations conformational flexibility multiple protonation states is given Thirdly results from our internal suite of test cases are presented Finally a practical tutori
215. com USPS Schr dinger 1500 SW First Ave Suite 1180 Portland OR 97201 Phone 503 299 1150 Fax 503 299 4532 WWW http www schrodinger com FTP ftp ftp schrodinger com Generally e mail correspondence is best because you can send machine output if necessary When sending e mail messages please include the following information most of which can be obtained by entering SCHRODINGER machid at a command prompt All relevant user input and machine output Jaguar purchaser company research institution or individual Primary Jaguar user Computer platform type Operating system with version number Jaguar version number Maestro version number mmshare version number Jaguar 6 0 Quick Start Guide Appendix A Copyright Notices A 1 NCSA HDF5 Software Library and Utilities Copyright Notice and Statement for NCSA HDF5 Hierarchical Data Format 5 Software Library and Utilities NCSA HDFS5 Hierarchical Data Format 5 Software Library and Utilities Copyright 1998 1999 2000 2001 2002 2003 2004 by the Board of Trustees of the Univer sity of Illinois All rights reserved Contributors National Center for Supercomputing Applications NCSA at the University of Illinois at Urbana Champaign UIUC Lawrence Livermore National Laboratory LLNL Sandia National Laboratories SNL Los Alamos National Laboratory LANL Jean loup Gailly and Mark Adler gzip library Redistribution and use in
216. coo o oo Uoc oO GO oO oo oO ww WW o oO WAS W Cc OC OC u O ul OD N Oo Go oorumuo 399928 oo UO OC OG OO Ul o oOONDNDNDO oorrro C c ca oO 4 O OG 8 235 OOO WW WW OO UU NY WwW oc OO Ww tu O GNUO amp oohuuo gt O oo O O OG 828 O O O 9 258 oo uU WN amp COrRRRO O O XO OG COO UO O O G WWW O OW lt i T Ge O O wa w C O u NO oO oohuuo CX XO XO O O GOG Co COGO UO c orb NIE OG oorrro oo b IN DO 10 4 The Grid File The grid input file grid file determines the grids used during the calculation Each grid type for example coarse or ultrafine is constructed from grids assigned to each atom in the molecule For any basis set for which the pseudospectral method is used the grid file must contain grids for each grid type used where each of these grid types in turn requires atomic grids for each element in the molecule Grids can be assigned to grid types in the input file using the gen section keywords gcoarse gmedium and so on 10 4 1 File Format and Description The first line of a grid file contains a character string which includes the version number of Jaguar This string should be gridv followed immediately by four digits giving the version number times 100 Leading zeroes are added if necessary The next line should consist of an integer which gives the number of grid types described in the file For instance this number would be six if the grids specified were of the types coarse medium
217. cript is in your PATH If the installation directory is different on different hosts for example if you have a Linux cluster on which SCHRODINGER opt schrodinger and a desktop computer on which SCHRODINGER software schrodinger you must make the SCHRODINGER setting depen dent upon the value of HOSTNAME in your shell startup scripts so that the correct installation directory is located on each host 13 1 2 4 Selecting Nodes for a Job Job queuing software such as PBS is often used on computer clusters to assign nodes and manage the load If you are not using job queuing software you can select the nodes that a job will run on in the following ways Select the nodes using the HOST option of the jaguar run command The list of nodes must be enclosed in quotes Create a local machines LINUX file listing the nodes you want to use and set the envi ronment variable SCHRODINGER NODEFILE to point to this file Create a local machines LINUX file listing the nodes you want to use and set the SCHRODINGER MPI FLAGS environment variable to machinefile filename The file name must be the full path to the file Use of the HOST option overrides the use of the environment variables If the local host is in the list of available nodes the controlling MPI process runs on the node from which you execute the jaguar run command otherwise it runs on the first node in the node list 13 1 2 5 Troubleshooting Parallel Job Problems
218. cros panel from the Edit menu in the main window 2 From the Macro Key option select a function key F1 through F12 to which to assign the macro 3 In the text box type the commands for the macro 4 Click Run to test the macro or click Save to save it 5 To run the macro from the main window press the assigned function key For more information on macros see Section 12 5 of the Maestro User Manual 2 8 Specifying a Maestro Working Directory When you use Maestro to launch Jaguar jobs Maestro writes job output to the directory speci fied in the Directory folder of the Preferences panel By default this directory the file I O directory is the directory from which you started Maestro To change the Maestro working directory 1 Open the Preferences panel from the Maestro menu 2 Click the Directory tab 3 Select the directory you want to use for reading and writing files Jaguar 6 0 User Manual 25 Chapter 2 Introduction to Maestro 26 Preferences prefer EH nix N Font Size Project Directory Label Mouse File Sufix Builder Feedback Default directory for job startup and file i o Maestro s current working directory Parent of project directory v Project directory v Project jobs directory Other specify below eurrentdir Close Help Figure 2 6 The Directory folder of the Preferences panel You can also set other preferences in the Preferences panel See
219. ction 47 Keyword econv in the gen section 48 Keyword dconv in the gen section Jaguar 6 0 User Manual 69 Chapter 4 Options 70 graph is satisfied first the calculation ends even if the RMS density matrix element change criterion has not been met and vice versa 4 8 3 Convergence Methods Jaguar provides a range of options for controlling the convergence of SCF calculations These options are available in the Convergence methods section Level shifting adds a constant to the diagonal of the Fock matrix for the virtual orbitals before diagonalization This reduces the mixing of the occupied and virtual orbitals and damps the changes in the orbitals As a result the convergence is slower but this method often helps otherwise intractable cases to converge Level shifting is normally varied during the course of an SCF calculation without having to explicitly set a value Useful SCF level shift values are generally in the range 0 3 1 0 You can set the constant in the SCF Level shift text box Thermal smearing populates the virtual orbitals using a Fermi Dirac distribution with a given temperature allowing orbitals other than the default orbitals to be populated The temperature is progressively reduced so that the true occupied orbitals are the only ones populated at the end of the calculation This procedure makes it easier for orbitals to switch if they are not in the default initial guess but are in the converged wave fun
220. ction To use thermal smearing choose a method from the Thermal smearing option menu and enter a value in the Initial temperature text box More information on this method can be found on page 205 Finally you can attempt to force convergence by selecting the Force convergence option This option starts with a large level shift and adjusts the value during the calculation and runs at ultrafine accuracy level Use this option with caution To speed up convergence Jaguar uses one of a number of convergence acceleration schemes which are available from the Convergence scheme option menu We recommend using the default Direct Inversion in the Iterative Subspace DIIS or GVB DIIS SCF convergence schemes 11 110 whenever possible The DIIS method generally performs better but for jobs with SCF convergence problems GVB DIIS may give improved convergence The DIIS method can be used with any wave function including those with multiple open shells and multiple GVB pairs You can also use the OCBSE convergence scheme 20 although it is generally much slower than DIIS 49 Keyword vshift in the gen section 50 Keyword ifdtherm in the gen section 51 Keyword fdtemp in the gen section 52 Keyword iacscf 1 in the gen section 53 Keyword iconv 1 in the gen section 54 Keyword iconv 4 in the gen section 55 Keyword iconv 3 in the gen section Jaguar 6 0 User Manual Chapter 4 Options 4 8 4 Orbital Treatment Converg
221. ction immediately Display Open a panel or dialog box Object Type Choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit The object type is marked on the menu with a red diamond and the button is indented to indicate the action to be performed Other Setting Set a state choose an attribute or choose a parameter type and click on atoms in the Workspace to act upon that parameter Atoms Distance Residues Angle Chains Dihedral other setting ject typ parameter type Molecules Chirality I Entries Delete Adjustments action Select display Figure 2 2 The Workspace selection button menu and the Adjust distances angles or dihedrals button menu Jaguar 6 0 User Manual 7 Chapter 2 Introduction to Maestro The Toolbar Buttons The toolbar buttons are described below Some descriptions refer to features not described in this chapter See the Maestro User Manual for a fuller description of these features Workspace selection Choose an object type for selecting Open the Atom Selection dialog box Open a project Open the Open Project dialog box Open Close Project Table Open the Project Table panel or close it if itis open Create entry from Workspace Open a dialog box in which you can create an entry in the current project using the contents of the Wor
222. ctor is entered in the tvec section it defines the forward direction An example of such a vector is as follows amp tvec C2 H3 05 Ol 22 H3 o 21 0 amp This definition produces a composite coordinate that is the sum of 0 5 times the distance between atoms C2 and H3 and 1 0 times the angle O1 C2 H3 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Coordinates comprising this composite can be any combination of bond stretches 2 atoms listed angle bends 3 atoms and dihedral angles or torsions 4 atoms Atom labels or index numbers for the atoms can be used in specifying atoms Coordinate coeffi cients specified by including an asterisk followed by a value after the last atom are optional The default coefficient value is 1 0 The forward direction is the direction that makes the composite coordinate defined in this section larger 3 The Hessian eigenvector for the imaginary frequency mode with the most negative eigen value of the Hessian is used to define the forward direction The phase of the eigenvector is chosen so that the largest coefficient is positive and the forward direction is the direc tion that increases the coordinate for the largest coefficient IRC calculations can be done in either Cartesian coordinates specified with intopt 0 or redundant internal coordinates intopt 1 which is the default Table 9 23 Keywords for IRC calculations Keyword Value Description irc
223. ctor of the Hessian and to minimize along all other coordinates This process is well defined and straightforward when the Hessian has exactly one negative frequency indicating that the structure is near a saddle point The negative eigenvalue mode which is sometimes known as the reaction coordinate is referred to as the transition vector in this chapter 5 3 2 Specifying Structures for the Reaction Structure selection for transition state searches operates differently from structure selection for other tasks The controls at the top of the Jaguar panel are not available Instead you select structures for the reaction from the entries in the Project Table using the controls in the Struc tures section of the Transition State folder When you choose a search method the controls for selecting the structures that you must provide become available You can either type the entry name in the text box or click Choose to open an entry selector and select the entry To display any of these structures in the Workspace click the inclusion button to the left of the entry name The diamond is checked when the structure is displayed Click the button again to undis play the structure The structures that you specify for the reaction must have the atoms listed in the same order One way of ensuring the correct ordering is to build one structure in Maestro then modify it to generate the other one or two For an example see the Jaguar Quick Start Guide If the
224. ctral method described above for the majority of the compu tationally intensive two electron integral terms but calculates the one electron and some of the largest and most efficiently computed two electron terms analytically 13 For the Coulomb matrix elements we calculate the analytic terms Y GAD y kl for cases in which i j k and meet certain cutoff criteria and the two electron integral ijlkl is of the form aalaa aalab aalbb ablab or aalbc where a b and c indicate the atom upon which the function is centered Similar correction terms are computed for the exchange operator as detailed in ref 13 The corresponding pseudospectral terms as defined by Equation 3a and Equation 3b for the appropriate choices of i j k and must be subtracted from the pseudospectral J and K elements as well This combined pseudospectral analytic approach allows Jaguar to take advantage of the strengths of both methods since it can largely maintain the pseudospectral method speedups for a particular grid and can also use a coarser grid than a purely numerical calculation would allow 8 2 Pseudospectral Implementation of the GVB Method The pseudospectral method has also been extended to electron correlation methods particu larly for Generalized Valence Bond GVB 20 calculations Highly refined GVB initial guess 14 and convergence 11 algorithms have been automated within Jaguar allowing the scaling advantages of the pseudo
225. culations using protocol 2 OPTIONS basis cc pvtz dftname x3lyp icfit 1 WORKDIR protocol2 OUTDIR protocol2 SJOB JOB proto2 To run this script for the files in the subdirectory structures you would use the command jaguar batch template bat structures in The input files are copied from the structures to the directory specified by WORKDIR modi fied with keywords and renamed as specified in the batch script and then submitted to Jaguar The output file the log file and the restart file are written to the directory specified by OUTDIR Jaguar 6 0 User Manual Chapter 12 Troubleshooting Naturally we hope that you will never need to use this chapter However if you have problems using Jaguar you may find useful advice here If you don t feel free to contact us as described on page 334 For problems with settings you might find the information you need in the online help You can obtain help from any panel by clicking its Help button The Help panel is displayed with the appropriate topic selected 12 1 Problems Getting Started If you are having problems starting Maestro or submitting jobs read this section Your local system manager should have already installed Jaguar If the command SSCHRODINGER maestro amp does not work because the maestro command does not exist or if you get an error message regarding installation contact this person The exact wording of error messages you get when trying to run Jaguar mi
226. current state of the input file to disk Write and to cancel all your changes without closing the dialog box Revert The Edit menu provides Cut Copy and Paste options for cutting and pasting within Maestro but you cannot use these to copy text from another applica tion To copy and paste text from another application or from Maestro highlight the text then Edit Job File Edit Structure Edit Input File 4 Structure 2002314708000 7951057678000 041478355300 3206721010000 6052771144000 005536787100 1678722364000 4091648794000 033561614100 1053831025000 8127361885000 036754469100 2257902210000 5875734174000 000802832300 0730021844000 3914970293000 038321021000 0967963987000 4204434914000 071897410000 3108964998000 0692396240000 007996805500 2615870999000 4982390021000 061531589500 0019410769000 4380876308000 067220362400 2159506374000 0514731434000 003269288100 1666842277000 4805803881000 066300674200 OK Cancel Preview Help Figure 3 2 The Edit Job dialog box with Structure selected Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro middle click where you want the text to be pasted The text in the paste buffer is saved when you close the dialog box so you can copy text between input files The Edit Job dialog box has two editing modes Input File and Structure By default the entire input file is available for editing In Structure mod
227. d as arguments to the jaguar batch command For example for the job speci fication h2o h2o_dft dftname b3lyp the file h20 in is read the keyword setting d tname b31yp is added to the gen section of the input and the new input is written to the file h2o_dft in The same effect is achieved with the job specification SJOB SJOB dft dftname b31yp and running jaguar batch with the job name h2o as an argument If no options are specified the Jaguar job is run using the template file as input For example if you had a set of input files jobnamel in jobname2 in jobname3 in you could use the following batch input file to run Jaguar for each input file in order Jobnamel Jobname2 Jobname3 Options for each Jaguar job can be set in preceding OPTIONS directives or by an options list appearing in the job specification An options list appearing in the job specification applies only to that job Options specified in an OPTIONS directive apply to all subsequent jobs unless superseded by a later OPTIONS directive or by the options list for the job These job options can specify any of the following items for the relevant jobs Keyword settings in the gen section of the Jaguar input file Paths and names of data files such as the basis set file or the grid file Sections to remove from the template input file for example the guess section if you are changing basis sets or the gvb section if you are comparing GVB results to HF LMP
228. d for an optimization Jaguar performs the opti mization using Cartesian coordinates rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry 5 2 3 Applying Dynamic Constraints Dynamic constraints also called soft or harmonic constraints are implemented by means of Lagrange multipliers A dynamic constraint on a geometric coordinate is met gradually during the course of an optimization One advantage of using a dynamic constraint on a vari able is that you can choose a value that is different from its current value For example if you have a complex structure whose conformation you want to change and you know that Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans changing a particular torsional angle would cause parts of the molecule to crash into each other if the torsional angle s value were suddenly imposed you can instead specify the desired value for the torsion as a dynamic constraint The optimizer changes the torsion gradually during the optimization so that the final torsional angle is as close as possible to the desired torsional angle Defining dynamic constraints is handled in the coord section which is described in Section 9 4 on page 172 You can make a constraint dynamic by editing the input file or by using the controls in the Optimization folder To make a constraint in the Constraints table dynamic select the table row then select Dynami
229. d links to Third Party Programs and Linked Sites do not constitute an endorsement of such Third Party Pro grams or Linked Sites January 2005 Contents Document Conventions een xiii Chapter T Introducti DIT aan 1 Chapter 2 Introduction to Maestro diu rdv roto dicas 3 2 1 General Interface Behavior sse 3 VALE CIPIT Cet 3 2 3 The Maestro Main Window esesseeeeeneeeeneeenneneenen nen 4 2 9 1 The MOnDuBAE oir ieu een 6 2 3 2 Ihe TOOIDSE iib getto Leiter ba it late dust apa Usu Ap tite Es se ind cape 7 2 3 3 Mouse Functions IN the Workspace 10 2 3 4 Shortcut Key Combinalions toit iiti big ertet dee epiac bodie ies Po Ub iseaibens 11 2 4 Maastro Projects oe AD FARE AD UR PNE REIR ER RIP PAPER PE MEDIE 11 2 4 1 The Project Table Toolbar uns ae 13 2 4 2 The Project Table Men s estate tto bae tta ba lan 14 24 3 elecliFiti I DIM BS tus 15 2 4 4 Including Entries in the Workspace eene 15 2 4 5 Mouse Functions in the Project Table sesseeeeeeeeeenennene 16 2 4 6 Project Table Shortcut Keys eat 17 2 5 Building a Structure nennen 18 2 5 1 Placing and Connecting Fragments eeeeeeeeenee 18 2 5 2 Adjustinig Properties iioii ud tres utei annsa tet codes dte iS ie tL hag Masbate 20 2 5 9 The Build Panel TOO als tz itera siete ito ee Sd Mb S LEAD sie tide 20 2 6 SOLS CHING TONS u B
230. d program sequences and instead allows you to concentrate on the science Try the sample calculation in Section 3 1 to get some experience running Jaguar and to make sure your system is set up properly If you have problems starting or using Maestro or performing the calculation you may be able to solve them using the troubleshooting sugges tions in Chapter 12 If any problems persist contact your system manager or Schr dinger The rest of this chapter describes the basics of running Jaguar from Maestro including entering a geometry and submitting a job Jaguar has a wide range of options for different kinds of calculations Setting these from Maestro is described in Chapter 4 Jaguar can perform many kinds of calculations such as geometry optimizations transition state searches and various coordinate scans Setting up these calculations is described in Chapter 5 Jaguar also provides special capabilities for pK prediction and accurate calculations with J2 theory J2 theory calculations are described in this chapter pK calculations are described in Chapter 14 The footnotes describe Jaguar input file keywords and sections that correspond to particular GUI settings If you are working from Maestro you can ignore these footnotes but you may later find them helpful if you decide to use input files to submit jobs without using Maestro or if you want to edit keywords directly using the Edit Job dialog box 3 14 Sample Calculation This sec
231. d the command jaguar results energy RuCp2 out piperidine out from a directory containing the output files RuCp2 out and piperidine out you would get a very simple table like this 480 726524 250 470399 Jaguar 6 0 User Manual Chapter 6 Output where the first line lists the final energy from the job RuCp2 and the second lists the final energy from the job piperidine If you use the option title the table has column headings indicating the type of information listed The columns appear in the table in the same order they are listed in the jaguar results command For instance the command jaguar results title jobname method energy h2o out h20 b3lyp out where h2o out and h2o b3lyp out are output files from jobs at the Hartree Fock and B3LYP density functional theory levels respectively gives the table Jobname Method Energy hartree h2o HF 76 023641 h2o_b3lyp B3LYP 76 418721 with the job name method and energy listed from left to right in the same order they were in the jaguar results command If you want to see ahead of time what the column headings of your table would look like without any results listed use the titleonly option The Jaguar results tables can list both information describing the job run for instance its name the basis set and SCF method used or the stoichiometry of the molecule and informa tion about the results of the job for example the final energy or dipole moment Each
232. d under the icut heading Cutoff sets are explained in the cutoff file description in Section 10 5 on page 257 The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M fine F or ultrafine U See Section 9 5 24 on page 218 and Section 10 4 on page 254 if you want more information on grids and grid types Jaguar 6 0 User Manual 113 Chapter 6 Output 114 The total energy for the molecule in Hartrees appears in the next column followed by the energy change from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one In the last column the maximum DIIS errors listed provide a measure of convergence by listing the maximum element of the DIIS error vector For HF and DFT closed shell calcula tions the DIIS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 After the energy information for each SCF iteration a summary of the components of the final converged energy is given Each of these energies is labeled with a letter for example A for the nuclear repulsion and information to the right of some of the energies describes the rela t
233. dated file and resets the name to default cutoff This chapter contains descriptions of the basis atomic initial guess dealiasing function grid cutoff and Lewis files Even if you do not plan on creating your own versions of these files you might want to skim this chapter if you are curious about the methods used in Jaguar 10 1 The Basis Set File The basis sets available for use in Jaguar appear in the file default basis in the standard data directories Portions of this file are shown in this section you might want to refer to them as you read the description of the file Basis sets at the top of the file do not contain effective core potentials and will be described first The basis sets with effective core potentials whose names begin with LA will be described later 10 1 1 Basis Set Format Each basis set description begins with a blank line The next line or lines must begin with the word BASIS followed by one space That label is followed by one or more names of the basis set to be described the name of the basis set as given in Table 4 1 on page 56 or Table 4 2 on page 58 and any other names which describe the same basis set e g STO 3G and STO3G The basis set names are separated by commas and must include and or characters if those Jaguar 6 0 User Manual 243 Chapter 10 Other Jaguar Files 244 are allowed for that basis set or character strings are sufficient to describ
234. density functional theory DFT G GAMESS input files keyword for een 215 ojo rto rin ro UY 139 GAUSSIAN Hessian format eee 234 orbital output in format for 141 217 GAUSSIAN basis set file gbs keyword for generation Of 215 Gaussian function list in output keywords 212 GAUSSIAN input file gau keyword for generation of 152 215 option for generation of 138 151 153 generalized gradient approximation 165 Generalized Valence Bond method see GVB calculations geometry input sese 35 41 Cartesian format 36 37 170 format een 170 174 input file sections 170 174 Keywords essen 174 output file echoed in 110 sample calculation symmetrizing seese troubleshooting eene units keyword for Z matrix format geometry optimization calculating forces only 186 constraining bond lengths or angles 40 90 92 172 constraining Cartesian coordinates 37 91 92 convergence criteria 88 89 119 191 coordinate system nuenesesnenesnennenennenenennenn 90 detailed output option for 137 frozen bond lengths or angles for 40 90 92 172 frozen Cartesian coordinates for 37 91 92 GDIIS method niece 187
235. der noi ro eret 136 output Options eeeeeeeenernnenn 114 142 atomic units eie o ehe 137 bond lengths and angles 137 connectivity table sess 137 detailed timing information 136 echo input file and parameter list 135 files toes etes 138 139 214 215 Gaussian function list 138 geometry optimization details 137 memory disk and i o information 135 one electron Hamiltonian 138 Orbital ainiin 139 142 215 218 Overlap MaRe i e eerte 138 per iteration iie ntes 215 216 standard 135 138 212 213 output summarizing 0 eee 105 110 output see output file output options standard output file output options per iteration output options orbitals babel overlap matrix in DIIS error vector 114 143 keyword for eigenvector and eigenvalue out J 213 keyword for output of 213 output option 138 smallest eigenvalue listed in output 111 Index P parallel execution n ritirare 306 frequency jobs ne nre he 297 jobs that can t be run sess 297 optimum processor number 306 selecting number of CPUS 49 parallel Jaguar module IBM installation eee 304 installation ttt 297 Linux installation
236. describe the cutoff sets used for the first and updating iterations in the final sequence respectively Finally the last column dictates the cutoff sets used for non SCF calculations as for gradient calculations The first six lines of the default cutoff file which illustrate these points are cutv0300 1177177 max accuracy prelim prelim update final final update gradient 3 147 accurate 56268 quick solvent 0 00 0 0 00000 The rest of the cutoff file consists of the cutoff sets Each set is specified by one line with four integers sometimes followed by lines containing explicit cutoff keyword values and ending with a blank line The four integers represent the variables jcor and kcor described below the grid number and the number of cutoff values to follow immediately below The grid number should be 1 for the coarse grid 2 for the medium grid 3 for the fine grid and 4 for Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files the ultrafine grid 5 for the charge grid 6 for the gradient grid 7 for the electron density cubic grid 8 for the DFT medium grid or 10 for the DFT gradient grid where these grids are speci fied by the keywords gcoarse gmedium gfine gufine gcharge ggrad geldens gdftmed and gdftgrad Section 9 5 24 on page 218 contains more information on these keywords The next lines specify each cutoff by number e g 22 for the variable cut22 and value Thus the cutoff set 52423 set
237. dicate the Jaguar input file keywords and sections that correspond to particular GUI settings If you are working from the GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI or if you want to edit keywords directly by using the Edit Job window described in Section 3 3 on page 34 5 1 Geometry Optimization The Basics To perform a geometry optimization you need a guess at the geometry and the direction in which to search a set of coordinates to optimize and some criteria for when the optimization is complete The search direction is obtained from the gradient of the energy and the initial Hessian The general settings for geometry optimizations are in the Optimization folder of the Jaguar panel Figure 5 1 This folder is present for all of the tasks listed above except Rigid Coordinate Scan for which no optimization takes place Four of the tasks have folders in which settings are made that are specific to the task These folders Transition State Scan and IRC are described in later sections 1 Keyword igeopt 1 in the gen section 2 Keyword igeopt 2 in the gen section 3 Keyword irc 1 in the gen section Jaguar 6 0 User Manual 87 Chapter 5 Optimizations and Scans 88 5 1 1 SCF and Geometry Convergence During geometry optimization Jaguar adjusts the convergence criteria for the SCF calculations at each geometry step for effic
238. diction Module Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation 4 nitroaniline 1 2 1 0 0 2 o toluidine 4 7 4 4 0 3 m toluidine 4 8 4 7 0 1 p toluidine 4 5 5 1 0 6 AMIDINES 2 3 5 6 tetrahydroimidazo 2 1 b thiazole 7 9 8 0 0 1 tetrahydrozoline 10 0 10 5 0 5 hydroxyimidazo 2 3 a isoindole 8 9 8 6 0 3 tolazoline 10 7 10 4 0 3 HETEROCYCLES pyridine 5 2 5 2 0 0 2 aminopyridine 6 9 6 7 0 2 3 aminopyridine 5 9 6 0 0 1 4 aminopyridine 9 3 9 1 0 2 4 methylpyridine 6 0 6 0 0 0 imidazole 6 6 7 0 0 4 benzimidazole 3 1 5 5 0 4 2 methylimidazole 77 7 9 0 2 4 methylpyrimidine 2 0 1 9 0 1 isoquinoline 5 4 5 4 0 0 pyrazole 2 5 2 5 0 0 quinoline 4 9 4 8 0 1 2 4 dimethyloxazole 6 0 6 0 0 0 thiazole 2 6 2 5 0 1 2 aminothiazole 5 5 5 3 0 2 2 methylthiazole 3 7 3 4 0 3 Jaguar 6 0 User Manual 323 Chapter 14 The pK Prediction Module Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation BENZODIAZEPINES 1 3 dihydro 1 methyl 5 phenyl 1 4 benzodiazepin 2 one 3 5 3 3 0 2 1 3 dihydro 3 hydroxy 5 phenyl 1 4 benzodiazepin 2 1 8 1 7 0 1 one 1 3 dihydro 3 hydroxy 1 methyl 5 phenyl 1 4 benzodi 1 3 1 6 0 3 azepin 2 one 1 3 dihydro 5 phenyl 1 4 benzodiazepin 2 one 3 8 3 5 0 3 2 3 dihydro 1 methyl 5 phenyl 1 4 benzodiazepine 5 9 6 2 0 3 GUANIDINES clonidine 8 1 8 1 0 0 debrisoquin 12 4 11
239. ding the cating the polarization functions e g 6 31G The first line for each atom type for that basis set should list three integers the atomic number for that atom type the number of uncontracted dealiasing functions about to be listed for each neighbor range in each set and the corre sponding number of contracted dealiasing functions In the sample file the first atom whose dealiasing functions are listed is hydrogen since the atomic number listed is 1 The same line says that ten uncontracted functions and two contracted functions will be specified for each range in the five sets of dealiasing functions for hydrogen characters indi The second line for the same atom type should list real dealiasing exponents for each uncon tracted function The exponents specify what functions can be used For instance in the sample file hydrogen s s type uncontracted basis function from the first exponent would be N e 9406347 while the p type uncontracted basis function for the same exponent would be N re 0406347 N and N are normalization constants Below those two lines the dealiasing function sets for that atom type should be listed set by set By default the first set will be used for the coarse grid the second for the medium grid and so on with the last set corresponding to the gradient This ordering can be changed in the gen section of the input file Each set should contain a line for each neighbor range the long rang
240. ds or dealiasing functions that do not match the new basis set If you change a basis set name to something Jaguar does not recognize runs using that basis set will use all analytic methods see Section 4 8 1 on page 68 or the information on the input file gen section keyword nops in Section 9 5 16 on page 201 To use the file in a Jaguar calculation you must add a line in the form BASISFILE filename to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format host fullpath or user amp host fullpath To make it easier to add basis sets to Jaguar a script called makejbasis has been provided that converts basis sets in GAUSSIAN 94 format as downloaded from the PNNL web site into Jaguar format The basis set download page of the PNNL web site is at http www emsl pnl gov forms basisform html When you download the basis sets you must save the data in text format not HTML format The syntax of the makejbasis command is SCHRODINGER utilities makejbasis input filename output filename Jaguar 6 0 User Manual 247 Chapter 10 Other Jaguar Files 248 where input filename is the name of the GAUSSIAN 94 format data file and output filename is the name of the Jaguar format basis set file The script is a Perl script If Perl is not installed in usr bin you can run this script by prefacing the command with per1 Because Jagua
241. ds with atoms of other ele ments except C atoms bonded only to C and or H and any pairs set in Imp2 section at LMP2 level other atoms at HF level ireson 0 Do not delocalize LMP2 pairs over other atoms 1 Calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of 7 atoms over neighboring atoms in the aromatic ring 2 Calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of lt 7 atoms over all atoms in the aromatic ring Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 7 Keyword settings for local MP2 calculations Continued Keyword Value Description idelocv 0 Do not delocalize any pairs listed in Imp2 section default for all calcula tions except those with iqst gt 0 and or ireson gt 0 1 Treat all LMP2 pairs but delocalize any pairs in Imp2 section as indi cated there or default for QST guided transition state searches delocal ize any pairs on atoms with breaking or forming bonds 2 Perform a local local MP2 calculation treating only pairs listed in the Imp2 section at the LMP2 level and also delocalize any pairs in Imp2 section as indicated there loclmp2c 0 Do not localize core orbitals for LMP2 calculation 1 Perform Boys localization on core orbitals for LMP2 calculation 2 Perform Pipek Mezey localization on core orbitals for LMP2 calculation ma
242. dule nannten 325 14 4 2 Running pK Calculations from Maestro eseeen 325 14 4 3 Jaguar Input Files for pK Calculations eseseeeeeeeneee 327 14 4 4 Running pK Calculations from the Command Line essesss 328 14 4 5 Monitoring pA Calculaflors i senken 329 14 4 6 Choice of Initial Geometrie une 330 14 5 Developing Your Own pK Correction Parameters 330 Chapter 15 Getting Help sc e 333 Noss ee dtc EN te ae 337 IIS deeRem TURN TUM S NRUR 347 Keyword INTER aaa dpa da ae do Gd GV RE iir c av dd 361 Jaguar 6 0 User Manual Document Conventions In addition to the use of italics for names of documents the font conventions that are used in this document are summarized in the table below Font Example Use Sans serif Project Table Names of GUI features such as panels menus menu items buttons and labels Monospace SSCHRODINGER maestro File names directory names commands environment variables and screen output Italic filename Text that the user must replace with a value Sans serif CTRL H Keyboard keys uppercase In descriptions of command syntax the following UNIX conventions are used braces enclose a choice of required items square brackets enclose optional items and the bar symbol separates items in a list from which one item must be chosen Lines of command syntax that wrap should be
243. e 32 jobname babel babel options nbo results options jobs jobnames jobids status all kill jobnames jobids Status purge jobnames jobids stop jobnames jobids status machid platform scripts sysreq help Start the Jaguar jobs whose job names are listed using the speci fied version information and run time options Start a Jaguar batch job using the specified script The optional job names specify input files for the script See Section 11 3 on page 282 for more information on this command Start a Jaguar pK calculation Start a Jaguar J2 calculation Perform a file format conversion using Babel Run an NBO calculation Summarize results from the output file using the options speci fied See Section 6 1 on page 105 for more information on this command Show the status of the specified running Jaguar jobs or list the jobs that have the specified status The all option shows the sta tus of all jobs including completed jobs The output lists the job ID the job name the status Kill the specified Jaguar jobs or all jobs that have the specified status This command is processed immediately Remove records for the specified jobs from the job database If no jobname is given all completed jobs are purged Stop the specified Jaguar jobs or all jobs that have the specified status when the currently running executable has finished Report the hardware and software configur
244. e only the geometry is displayed and a Structure menu is added to the menu bar If you are editing geometries for a transition state search or an IRC scan all three geometries can be edited The editing area has tabbed folders for each of these geometries labeled Reactant Product and Transition State The Structure menu provides options for modifying the geometry input The Convert to Z matrix and Convert to Cartesians options switch between Z matrix format and Cartesian format The option Assign Unique Atom Labels converts all atom labels to the form El where El is the standard element symbol Fe for iron for instance and Z is the atom number in the input list 1 for the first atom 2 for the second and so on This option guarantees that all atoms have unique atom labels which is required by Jaguar Unique atom labels are assigned automatically if Jaguar detects any ambiguity in the labels You can display the atom labels in the Workspace by choosing View Atom Labels The remaining option on the Structure menu is useful for transition state searches but not for other Jaguar jobs This option is described in Section 5 3 on page 93 The changes you make are automatically saved in the Maestro project and are reflected in the panel settings You can view the changes to the geometry in the Workspace by clicking Preview Note Counterpoise atoms constraints and coordinates for Hessian refinement should not be added in this dialog box they a
245. e the 150 conformation of glycine is N1 2 N1 1 4589 C3 C2 1 5203 N1 115 32 04 c3 1 2036 c2 126 28 N1 150 0 05 c3 1 3669 C2 211 39 N1 31 8 H6 N1 1 0008 C2 113 55 C3 69 7 H7 N1 1 0004 C2 112 77 3 5729 H8 c2 1 0833 N1 108 89 H6 170 0 H9 C2 1 0782 N1 110 41 H6 52 3 H10 05 0 9656 C3 171 63 C2 178 2 3 4 5 Variables and Dummy Atoms in Z Matrix Input Bond lengths or angles can also be specified as variables below the Z matrix itself This feature makes it easier to input equal values such as C H bond lengths or H C H bond angles for methane and also makes it possible to keep several distances or angles the same as each other during an optimization To use variables type the variable name chbond for instance where you would type the corresponding value such as a C H bond length in for each relevant occurrence of that value You can prefix any variable with a or sign After you type the full Z matrix define the variables by adding one or more lines at the bottom such as chbond 1 09 HCHang 109 47 As for Cartesian input you can separate the variable settings from the coordinates by a line containing the text Z variables Defining dummy atoms can make the assignment of bond lengths and angles easier Dummy atoms are a way of describing a point in space in the format used for an atomic coordinate without placing an atom at that point The symbols allowed for dummy atoms are X or Du An example of the use of a dum
246. e Fields SQM method 63 for B3LYP calculations using the 6 31G basis set and standard frequency scaling in which all frequencies are simply multi plied by a single parameter Jaguar 6 0 User Manual Chapter 4 Options The SOM method alters the frequencies by scaling the Hessian elements themselves in internal coordinates using 11 different scale factors which depend on the type of stretch bend or torsion This method was parametrized using B3LYP calculations for 30 molecules containing C H N O and CI using the 6 31G basis set Jaguar permits the SOM scaling method to be used only for B3LYP 6 31G frequency jobs You can turn on SOM scaling by selecting Pulay SQM method B3LYP 6 31G factors The method is off by default Alternatively for any type of frequency job you can multiply all frequencies by the same scale factor by selecting Scaling factor and selecting a combination of method and basis set from the option menu or selecting User defined from the option menu and entering a factor in the text box Table 4 4 lists the recommended scale factors for various methods and basis sets These factors are used when you make a selection from the option menu The factors in the table are from Ref 64 and are optimized for the best agreement with experiment for the frequencies themselves Ref 64 also includes scale factors suitable for use when low frequency vibrations are of particular interest for zero point vibrational
247. e Jaguar Input File 212 Table 9 31 Output format keywords and file types for babel file format conversions Continued Format Keyword File Type maccs MDL Maccs file torlist Torsion List file tinker Tinker XYZ file unixyz UniChem XYZ file xyz XYZ file xed XED file For either babel or babelg keyword settings you can use an optional extra extension for the file name by setting babel or babelg to a keyword in the form outext opt where opt is any extension you want to use For instance if you made the setting babel gzmat gau in a Jaguar input file called h2o in the resulting job would create a Gaussian input file called h2o gzmat gau You can also convert file formats from the command line using the jaguar babel and jagconvert utilities See Section 11 2 5 on page 278 for information on these utilities 9 5 20 Standard Output Keywords The keywords listed in Table 9 32 are the standard print options They are all set to 1 by default and the result is that none of the information that the keywords select is printed Many of the print options can be turned on from the GUI as described in Section 6 4 on page 135 The keyword setting ip6 3 provides much more detailed timing information than the setting ip6 2 Similarly the keyword setting ipl92 3 provides more detailed output than ip192 2 the ip192 3 setting includes the Hessian The keyword setting kesep 1 which is normally part of a solvation calculation see Table 9
248. e Optimization folder see Section 5 2 on page 90 5 3 3 Searching Along a Particular Hessian Eigenvector If you are using the standard non QST guided transition state optimization method you can specify a Hessian eigenvector for the optimizer to follow The choices of eigenvector are avail able from the Search along option menu Lowest Hessian eigenvector the default the Lowest non torsional mode the Lowest bond stretch mode or a User selected eigen vector You also have access to these search directions if you are doing an LST search in addition to the Reactant product path Under certain circumstances you might want to direct your transition state search using these options rather than having the optimizer simply minimize along the lowest Hessian eigen vector found for each iteration The Lowest non torsional mode and Lowest bond stretch mode options can be useful for steering the optimizer to a particular type of transition state for instance for a study of a bond breaking reaction you can avoid converging to a torsional tran sition state by choosing Lowest bond stretch mode If you know the index number of the eigenvector along which you would like to minimize a particular bond stretch for instance you can make the optimizer follow that eigenvector by choosing User selected eigenvector and specifying the eigenvector number in the Eigenvector text box gt You can identify the index number by running one
249. e any geometry dependent settings a Jaguar batch script is created to run the calculation on each structure Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Jaguar jaguar Start Output Incorporate Replace existing entries Job Name benzene Host localhost 1 CPUs 1 Scratch directory scr i Start Cancel Figure 3 6 The Start dialog box You can submit a job either from Maestro or from the command line Information on submit ting jobs from the command line with the jaguar run command can be found in Section 11 2 on page 272 This section describes the submission of jobs from Maestro Regardless of what kind of job you run or where the input is obtained from you can submit the Jaguar job by clicking the Start button in the relevant panel The Start dialog box Figure 3 1 is displayed in which you can enter information on how and where to launch a job This dialog box has two sections the Output section and the Job section 3 9 1 Output Handling In the Output section you can choose how the results are incorporated into Maestro at the end of the job using the Incorporate option menu The options are Append new entries add entries for the output structures and properties from the job to the end of the Project Table Replace existing entries replace the entries that you chose for the input with the output structures and properties from the
250. e atoms and that settings in the atomic section take precedence over Z matrix counterpoise input In the atomic section counterpoise atoms are indicated by using an entry of n in the column enti tled charge see Table 9 46 Also note that any other word or letter such as the Y entries that may appear in restart files indicates that the grid dealiasing function or charged particles for that atom are included the usual default for the grid daf and charge keywords Table 9 46 Keywords for listing basis grid dealiasing function and charge information for indi vidual atoms in an atomic section Keyword Value Description basis n no or none Use no basis functions on atom basis name Use basis functions from specified basis set on atom grid n DO or none Do not include any grid points on atom only Include grid points on atom but no basis functions dealiasing functions or nuclear charge daf n no or none Do not include any dealiasing functions on atom only Include dealiasing functions on atom but no basis functions grid points or nuclear charge charge n no or none Treat atom as a counterpoise atom do not include nucleus or elec trons for atom only Include nuclear charge on atom but no basis functions grid points or dealiasing functions 9 8 4 Defining Fragments You can use the frag keyword in the atomic section to specify that all atoms with the same frag entry be treated in t
251. e final Hessian from the last geometry step as the initial Hessian for the next step 1 Use the Hessian specified by the inhess setting as the initial Hessian for the next step The Hessian in a hess section is only used for the first step unless inhess is explicitly set to 2 scanguess 0 For geometry scans use converged wave function from previous step as initial guess for current geometry 1 For each step in a geometry scan generate the initial guess wave func tion according to the iguess setting 9 5 11 Intrinsic Reaction Coordinate IRC Keywords IRC scans have been implemented in Jaguar using the methods described in Ref 149 The implementation includes IRC and minimum energy path MEP calculations The calculations start at a transition state and move downhill in energy along the reaction path toward a minimum of the potential energy surface They are mainly used to check that the given transi tion state is indeed the expected transition state for the reaction of interest The keywords for IRC and MEP calculations are listed in Table 9 23 The forward and reverse directions are defined as follows The first set of conditions that constitutes a valid definition is used 1 If two additional geometries are entered in the zmat2 and zmat3 sections they are assumed to be the geometries for the reactant in zmat2 and product in zmat3 The for ward direction is defined as moving from reactant to product 2 If a ve
252. e functions should be specified first then the home atom functions then the functions for each neighbor range in increasing order Within each line there should be several integers one for each uncontracted function then one for each contracted function These integers dictate how to construct the actual functions from the exponents just given in the da file for uncon tracted functions and already established in the basis file for contracted functions and contraction coefficients for contracted functions also established in the basis file If the Jaguar 6 0 User Manual 251 Chapter 10 Other Jaguar Files 252 value is 1 an s type function will be constructed using the relevant exponent or exponents if 2 a p type function if 4 a d type function if 8 an f type function and if 16 a g type function To construct more than one of these types of functions with the same exponent or exponents the relevant numbers should be added together for instance 1 2 4 7 for s p and d The exponent or exponents for each of these functions are determined by the position of the entry in the row The uncontracted functions are described first in the same order as their expo nents were listed earlier and the contracted functions corresponding to the contracted func tions found in the basis file are described next in the same order as in the basis set file Uncontracted functions in the basis set file should be ignored Fi
253. e initial wave function from orbitals that give the best overlap with previ ously calculated orbitals from atomic calculations The algorithm used is described in Ref 14 This method compares well with the semi empirical schemes that other ab initio programs use to obtain initial guesses Other methods for the initial guess can be selected with the iguess keyword including diagonalizing the one electron Hamiltonian which is rarely the best guess and using a superposition of atomic densities which provides a similar quality initial guess to the default However in cases where the default guess does not lead to the desired result this guess could provide an alternative that does Jaguar also provides a unique initial guess feature to improve SCF convergence both HF and DFT for transition metal containing systems which is based upon ligand field theory As described in Ref 19 research at Schr dinger has established that poor convergence of these systems is very often due to problems with the trial wave function s orbital shapes and occupa tions This initial guess method takes advantage of user provided information on charges and spins of fragments within the system as described in Section 7 1 3 on page 147 although such 1 Keyword iguess 10 in the gen section 2 Keyword iguess 0 in the gen section 3 Keyword iguess 11 in the gen section Jaguar 6 0 User Manual 145 Chapter 7 Using Jaguar 146 information is n
254. e scan coordinates the definition the type and the number of steps The total number of structures to be calculated is reported below the table and is the product of the numbers in the Steps column To set the values for the coordinate select the row for the coordinate in the table then enter the starting value the final value and the increment in the Selected Coordinate section The Current value and Number of steps text boxes are noneditable The number of steps is calcu lated from the values you provide Once you have defined all the coordinates and their values click Start to start the job or click Write to write out the input file for the job 5 4 2 Setting up Input Files for Scans To create an input file for a coordinate scan you set up an input file with the coordinates defined as variables and the variable values defined as described below For a relaxed scan the job must be a geometry optimization for a rigid scan it must be an energy calculation You can define a variable in the geometry input as described in Section 3 4 5 on page 39 or you can define variables in the coord section Using the coord section allows you to define variables that are not part of the Z matrix geometry input To define a variable in the coord section add the variable name after the sign in the coordinate definition For example the following input file section defines a coordinate HH as the distance between H1 and H2 amp coord Hl H2 H
255. e specified is inappropriate because of symmetry restrictions or other constraints the output will indicate the problem The geopt output then lists information on the current original geometry s gradient elements describes the small step it will use to alter the first coordinate used in the Hessian refinement describes the internal coordinates and optimization variables as stretches bends or torsions and indi cates how it generates a new geometry by altering the relevant coordinate by the amount described by the step size The new geometry generated for Hessian refinement is used to obtain energy and gradient information a process that requires the programs onee grid and rwr to run and generate output in the usual formats This is followed by output from the program scf which now starts with the calculation type and the table showing the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output continues with output in the usual formats from derla rwr and der1b The information obtained on that Jaguar 6 0 User Manual Chapter 6 Output geometry is then used in geopt which runs a second time reporting similar information about the planned changes to the molecular structure for the next Hessian refinement step if there is one and reporting the change in total energy from the original geometry to the geometry for the first Hessian refinement step as well This process
256. e structures are written to a single Maestro file and the Jaguar input files are created later by the batch facility To select pre existing files choose Selected structure files from the Source of structures option menu then enter a comma separated list of file names in the Files text box or click Browse The Browse button opens a standard file selector labeled Select Batch Inputs with the current directory and its files listed You can select either Jaguar input files or Maestro files for input If you select Maestro files Jaguar input files are constructed later To select multiple files use SHIFT to select a range of items and CTRL to select or deselect a single item without affecting other items When you have made a selection click OK The input files are passed to the batch script in the order in which they appear in the list To process input files in a particular order you must name them so that they appear in the correct order in the list After you finish selecting the batch script and input files click Start to launch the batch job The Monitor panel opens and shows the batch log file b1og for the batch job which logs the completion of each Jaguar job launched from the batch script The information is automatically updated as the Jaguar jobs run Jaguar 6 0 User Manual 51 Chapter 3 Running Jaguar From Maestro 52 3 11 Output A Jaguar log file contains comments on the progress of a job If the job was started
257. e the and cases also and the characters can be listed either before or after the characters The next notation in the line SD or 6D sets the default number of functions for d shells when using that basis set as described in Section 4 2 on page 55 Backup basis set names which are each preceded by the word BACKUP may follow on the same line If any sets are listed after the word BACKUP it indicates that if an atom is not found in the current basis set its basis function will be obtained from the list of backup basis sets If there is more than one backup name listed the basis function for the atom comes from the first backup set listed that contains that atom Note that the numbers of d shells specified in the backup basis sets is ignored Also polarization or diffuse functions are chosen according to the basis set specified by the calculation that is or options on backup basis sets are ignored if they do not agree with the options on the basis set chosen for the calculation The basis set description continues with a set of lines describing the basis functions on each atom The information for each atom begins with a line containing the element symbol e g He The atomic symbol must not be preceded by any spaces or characters The next line begins with the type of function S P or D for instance If this label is SP the corresponding set of data describes an s and a p function whose Gaussi
258. e unphysical for multiple bonds since they create multiple banana bonds between pairs of atoms rather than forming sigma like pi like and related orbitals The Boys orbitals for multiple bonds may therefore be diagonal ized using the one electron Hamiltonians The output for this procedure begins with a table of the Mulliken populations for each orbital on each atom which reveals multiple bonds as described in the following table Every bond pair space made up of all orbitals with signifi cant Mulliken populations on the same pair of atoms is diagonalized and the output indicates the number of these bond pair spaces found and the ordering of the new orbitals by their one electron Hamiltonian values If you choose to print out Boys orbitals by setting the print keyword ip107 to 2 it is these final orbitals which are printed Table 9 30 Keywords related to localization of orbitals Keyword Value Description locpostc 0 Do not localize core orbitals of final wave function 1 Perform Boys localization on core orbitals of final wave function 2 Perform Pipek Mezey localization on core orbitals of final wave func tion maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on core orbitals of final wave func tion maximizing Mulliken basis function populations 1 Mix the core and valence orbitals before localization then localize according to the locpostv setting Jaguar 6 0 User Manual Chapter 9 The Jagua
259. ection of the input file to 1 All analytic calculations use the cutoff keyword values in the cuto E file but ignore the jcor kcor and pseudospectral grid information Jaguar 6 0 User Manual 259 Chapter 10 Other Jaguar Files 260 10 6 The Lewis File The Lewis file determines how van der Waals radii for calculations using the Jaguar solvation module are set according to chemical functional groups By default for neutral molecules in water the program calculates a Lewis dot structure for the molecule or system scans the Lewis file for radius information for each atom and sets radii for relevant atoms then sets any radii not determined by the Lewis file according to the atomic section or the standard default value Settings for radii not included in the Lewis file are described in Section 4 9 on page 71 and Section 9 8 on page 226 and are listed in Table 9 44 on page 231 If you do not want the atomic radii that determine the dielectric continuum boundary to change according to the chemical environment of the atom set the solvation keyword isurf to 0 in the gen section Otherwise Jaguar will alter some radii for neutral molecules by using the default lewis file from the data directory unless you specify your own 1ewis file in a LEWISFILE line in the input file as described in Section 9 1 on page 167 If radii are set according to a Lewis file Jaguar first computes a Lewis dot structure for the input geometry to determine
260. ectral Algorithms for Electronic Structure Calculations Length Scale Separation and Analytical Two Elec tron Integral Corrections J Chem Phys 1994 101 4028 Langlois J M Yamasaki T Muller R P Goddard W A Rule Based Trial wave functions for Generalized Valence Bond Theory J Phys Chem 1994 98 13498 Tannor D J Marten B Murphy R Friesner R A Sitkoff D Nicholls A Ring nalda M Goddard W A IH Honig B Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory J Am Chem Soc 1994 116 11875 Murphy R B Beachy M D Friesner R A Ringnalda M N Pseudospectral Local ized MP2 Methods Theory and Calculation of Conformational Energies J Chem Phys 1995 103 1481 Lu D Marten B Cao Y Ringnalda M N Friesner R A Goddard W A III ab initio Predictions of Large Hyperpolarizability Push Pull Polymers Julolidinyl n isox azolone and Julolidinyl n N N diethylthiobarbituric acid Chem Phys Lett 1995 242 543 Murphy R B Pollard W T Friesner R A Pseudospectral localized generalized Meller Plesset methods with a generalized valence bond reference wave function Theory and calculation of conformational energies J Chem Phys 1997 106 5073 Vacek G Perry J K Langlois J M Chem Phys Lett 1999 310 189 Bobrowicz F W Goddard W
261. ecure server ports The mpich start command launches the secure servers on all of the hosts listed in the machines LINUX file To use the secure servers the following environment variables must be set csh tcsh setenv MPI_USEP4SSPORT yes setenv MPI_P4SSPORT port sh ksh bash export MPI_USEP4SSPORT yes export MPI_P4SSPORT port The port number assigned to MPI_P4SSPORT must match the port number used to launch the secure server These environment variables can be set up by root in the default environment or they can be set up in a login script to avoid having to set them manually at each session The last strategy does not work for ksh which does not execute a login script The mpich script can be used to manage the secure servers The syntax for the script is SCHRODINGER utilities mpich command options The available commands are listed in Table 13 1 and the available options are listed in Table 13 2 This script allows you to start and stop the servers on all or some of your machines and to check on their status through a single consistent interface The command acts on the hosts specified with the h option if any are given Otherwise it acts on the hosts listed in the machines file By default this file is the machines LINUX file from your MPICH installation You can override this default by specifying a file in the SCHRODINGER_NODEFILE environment variable or by using the m option The port on which the servers listen can
262. ed for that iteration but the density matrix was averaged The cutoff set for each iteration is indicated under the icut heading Cutoff sets are explained in the cutoff file description in Section 10 5 on page 257 The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M fine F or ultrafine U See Section 9 5 24 on page 218 and Section 10 4 on page 254 for more information on grids and grid types The total energy for the molecule in Hartrees appears in the next column followed by the energy change which is the difference in energy from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one Finally the maximum DIIS error column provides a measure of convergence by listing the maximum element of the DIIS error vector For HF calculations the DIIS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 If you are not running a default single point Hartree Fock calculation the log file generally contains information generated from other Jaguar programs used for the run as well This information is often a summary of what is written to the Jaguar output fi
263. ed numbers corresponding to each natural orbital and CI coefficient corresponding to each GVB natural orbital in the pair Next the overlap between the two corresponding non orthogonal orbitals for that pair is listed followed by the CI energy lowering which is a guide to the energy change resulting from the inclusion of the second natural orbital in the calculation If a GVB calculation is performed from a Hartree Fock converged wave function the program scf runs twice once to obtain the HF converged wave function and once to perform the final GVB calculation The SCF output from the first sc run will look like the SCF output from a standard HF calculation the output from the second run will have the format described above for a GVB calculation from an HF initial guess 6 3 4 Geometry or Transition State Optimization The output format description for optimizations in this subsection applies to calculations of either minimum energy structures or transition states Although the Hessians used during these calculations are different the Jaguar programs run are the same and the output format is very similar Exceptions are described below If you calculate an optimized molecular structure a transition state or forces any SCF calcula tions during the run use the RMS density change convergence criterion described in Section 4 8 on page 68 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed f
264. ed previously itrvec 0 Select lowest Hessian eigenvector as transition vector gt 0 Select eigenvector number itrvec as transition vector see Section 5 3 on page 93 Sets ifollow to 1 1 Select lowest non torsional eigenvector as transition vector 2 Select lowest stretching eigenvector as transition vector 5 Select eigenvector which best represents reaction path Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 19 Keywords for control of the Hessian Keyword Value Description inhess 1 Use Fischer Alml f guess for Hessian 0 Use Schlegel guess for Hessian default choice only if no hess section exists 1 Use unit matrix for initial Hessian 2 Use Cartesian input Hessian found in hess section inhess 2 automati cally if non empty hess section exists 4 Compute and use quantum mechanical Hessian irefhup 2 Refine initial Hessian using Powell updates 125 3 Refine initial Hessian using mixed Murtagh Sargent Powell updates 126 4 Refine initial Hessian using Murtagh Sargent updates 127 nhesref gt 0 Number of lowest frequency Hessian eigenvectors used in Hessian refinement default is 0 pertnd 0 05 Displacement in atomic units used for Hessian refinement or calcula tions of numerical forces or frequencies ihuptyp 0 Don t update Hessian 1 Update Hessian each iteration using BFGS Broyden Fletcher Goldfarb Shanno method 128 default for minimum energy structure optimiza tions 2 U
265. ee geometry input structure optimizing see geometry optimization structures building 18 21 displaying in sequence 13 selecting for IRC calculation 104 selecting for transition state optimization 95 submission host definition 271 submitting jobs see running jobs superblocks uueneeenensnnrnnn 204 Surface Table panel sss 86 surfaces displaying in Maestro sss 84 generating data for 84 222 symmetrizing geometry input 44 45 294 symmetry effect on structure esee 294 in IRC calculations 103 194 keywords ide 176 Maestro options 93 54 orbital populations eene 7 output information eene 110 specifying for GAUSSIAN input 152 use of in calculation 44 45 synchronous transit quasi Newton methods see QST guided transition state searches T technical support 28 temperatures for thermochemical calculations keywords tese sense 200 output s130 nq eines 83 temporary directory 49 293 after job is killed es 278 errors related to sss 292 293 m Output file 110 saving at end of JOB eee 276 specifying in hosts file 271 272 temporary files 5e nece ters 278 saving at end of JO
266. elding constants for atoms whose core is represented by an ECP should be treated with caution because the main contributions come from the core tail of the valence orbitals which is largely absent at ECP centers Chemical shifts derived from these shielding constants might display the correct trends but are likely to have the wrong magnitude 9 5 14 Frequency Related Keywords For jobs that include a calculation of vibrational frequencies various frequency related proper ties can also be computed by setting the appropriate keywords Most of these keywords which are listed in Table 9 26 correspond to GUI options described in Section 4 11 on page 79 Only the values listed in the table are allowed The thermochemical properties are listed in cal mol K and kcal mol by default Use the output option ip28 2 for output in J mol K and kJ mol Table 9 26 Keywords for frequency related properties Keyword Value Description ifreq 0 Do not calculate frequencies second derivatives 1 Get frequencies from Hessian of second derivatives of energy 1 Calculate frequencies from most recent Hessian from end of optimi zation or from initial Hessian if initial Hessian was never updated maxitcp 35 Maximum number of CPHF iterations rmscp 5x10 CPHF convergence threshold imw 0 Print normal modes in cartesian coordinates without mass weighting 1 Print normal modes in mass weighted cartesian coordinates isqm 0 Do not scale frequencies us
267. elow 0 005000 hartree State Rel Energy MOs 9 10 11 12 13 metal d occupations 1 0 00000000 2 1 1 0 0 2 0 00000224 1 2 1 0 3 0 00062053 2 1 0 1 0 4 0 00062276 1 2 0 1 0 5 0 00071513 2 1 0 0 1 6 0 00071737 1 2 0 0 i Jaguar 6 0 User Manual 111 Chapter 6 Output 112 WARNING The lowest energy configurations are degenerate The MO numbers with occupied metal d orbitals are given in the table above Jaguar will use the first configuration but you can select a different state configuration number from the table above with the istate keyword Using state configuration 1 2 1 1 0 0 In this example Jaguar has found six possible occupations of the five metal d orbitals that have essentially the same energy The table shows which MO numbers correspond to the metal d orbitals 9 13 in this example the occupation numbers 0 1 or 2 electrons per orbital and the relative energy in hartrees The lowest energy is the reference energy and is always 0 0 The probe program which follows hfig and ensures orthogonalization has no significant output The output for the grid generation done by the program grid lists the number of grid points for each atom as well as the total number of grid points for each grid used in the application of the pseudospectral method If you would like more information about these grids see Section 10 4 on page 254 The rwr program which generates the Q operators needed for the pseudospectr
268. emory available Table 9 16 Keywords for CIS calculations Keyword Value Description icis 0 Do not do a CIS calculation 1 Do a CIS calculation nroot 20 Number of roots to find Default value is 1 dconvci 1 0e 2 Convergence criterion for the norm of the residual CI vector default is le 5 for a non pseudospectral calculation Jaguar 6 0 User Manual 185 Chapter 9 The Jaguar Input File 186 Table 9 16 Keywords for CIS calculations Keyword Value Description econvci 1 0e 5 Convergence criterion for the change in energy default is 1e 8 for a non pseudospectral calculation nrestart gt 0 Number of CI diagonalization iterations before restarting 0 Determine number of CI diagonalization iterations before restarting automatically maxciit 32 Maximum number of iterations used for the diagonalization of the CI matrix 9 5 9 Geometry Optimization and Transition State Keywords Many of the keyword settings for optimization of minimum energy structures and transition states described in this subsection can be made from the GUI as described in Chapter 5 which also contains more details about the methods used for optimizations Table 9 17 contains general optimization keywords that apply to all kinds of optimizations Most default values for the integer keywords are indicated in bold italics and only the values listed in the table are allowed In cases where the default is different for optimizations to minimum e
269. en Ere tme 218 idft 179 184 idae een 176 ifdtherm seen 204 188 PEERS 199 Sadek EI PL E EE E FE US ERER FE AER RR READER 186 152 206 Breite t editi trien ra dE 206 235 s176 177 hag ELE LIEU DNE 176 177 POMPIERS NEUE 207 237 REPE 178 ONUS 176 206 Jaguar 6 0 User Manual 361 Keyword Index 362 IFCIBXCyC nicht 193 Irestep ne een 193 220 221 179 188 IFCBCut iio nmi etch 193 quii een TP RS 193 genui 193 Jaguar 6 0 User Manual wee 195 268 176 198 203 190 191 Mete UM one LL EI 190 U A 188 EWIGE m 204 last WV tecto ee E S ent H 220 lewdot 5 ene 176 177 178 lEWS nnn mener 176 177 195 268 lgrad Imedium loclmp2c loclmp2v Keyword Index M MUMS is 228 MASSIV ME 175 Maxita oro hs 186 MULAN US engines 201 203 newcon nhesref nmder nogdiis noopta nooptr inr noupdat eene DREStArt rE EES P pertnd eoe nets 187 189 plot mt eun dum 224 plotres 5 eee eire 223 DE6SS scere tr erre ees 200 Q QSUUN iis M 188 R radprb tetro 195 yii 199 S SCALE un 199
270. en section Jaguar 6 0 User Manual 73 Chapter 4 Options 74 4 10 Properties For each kind of wave function Jaguar can calculate various molecular properties The range of available properties depends on the wave function These calculations are normally performed using the converged SCF wave function By default none of the properties are computed but you can compute them by changing the settings in the Properties folder The Properties folder has a table of available properties and an area below the table where controls for a property are displayed when you select the table row for the property To include the calculation of a property in a job select the check box in the Calculate column Vibrational frequencies and related properties and surfaces are discussed in later sections This section focuses on the remaining properties 4 10 1 Charges from Electrostatic Potential Fitting Jaguar can fit the molecular electrostatic potential ESP to a set of point charges 58 59 These monopoles can be located either at the atomic centers or at the atomic centers and the bond midpoints depending on the selection from the Fit ESP to option menu The atomic charges are written to the output Maestro mae structure file and are available in Maestro as the partial charge These charges can then be used in other applications such as MacroModel or QikProp For electrostatic potential fitting of an LMP2 wave function you shou
271. en the atoms The next three numbers on each line give the x y and z Cartesian coordinates of the atoms in the geometry in angstroms The number of spaces you type does not matter as long as you use at least one space to separate different items When you finish entering the water geometry click OK To read in the structure click Read then navigate to the following directory SSCHRODINGER jaguar vversion samples where version is the 5 digit version number of your Jaguar software Select H20 in from the file list and click OK Whichever method of entry you chose the molecular structure should now be shown in the Workspace If you entered the geometry by hand the structure is a scratch entry You can run the job with a scratch entry but the results will not be incorporated into the Project Table unless you make it a named entry To do so click the Create entry from Workspace button in the toolbar and name the entry H20 in When you finish setting up your calculation click the Start button The Start dialog box is displayed see Figure 3 6 on page 47 In this dialog box you can make settings for running the job In the Output section you can select an option for incorporation of results Choose Replace existing entries In the Job section you can provide a job name select the execution host the number of processors and the scratch directory The entry name H2O appears in the Name text box The Jaguar 6 0 User Manual
272. en the plane formed by the first three atoms in this case N1 C2 C3 and the plane formed by the last three atoms in this case C2 C3 O4 Looking from the second to the third atom C2 to C3 the sign of the angle is positive if the angle is traced in a clockwise direction from the first plane to the second plane and negative if the angle is traced counterclockwise An alternative for specifying the fourth atom s position is to use a second bond angle instead of a torsional angle To specify another bond angle add 1 or 1 to the end of the line The second bond angle is the angle between the first second and fourth atoms in the example above the O4 C3 NI angle Since there are two possible positions for the atom which meet the angle specifications the position is defined by the scalar triple product rj r33 X r24 where rj r r is the vector pointing from atom j to atom i If this product is positive the value at the end of the line should be 1 If it is negative the value should be 1 You should use torsional angles Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro instead of second bond angles if you want to perform a constrained geometry optimization however since Jaguar cannot interpret any constraints on bond lengths or angles for geome tries containing second bond angles All additional lines of the Z matrix should have the same form as the fourth line The complete Z matrix for the example molecul
273. en virtual orbitals see the keyword ipvirt in Section 9 5 23 on page215 The virtual orbitals are obtained by diagonalizing Hoyt f 2J K where fis the fractional occupation of each orbital 1 for a closed shell The format for printing the selected orbitals can be chosen from the Format option menu The choices available are Large elements as f5 2 labels in list All elements as f10 5 labels in table All elements as f19 15 in list All elements as f8 5 in list All elements as e15 6 in table Examples of each of these style options appear below In the first option listed the phrase large elements indicates that only coefficients larger than a particular value generally 05 are listed The notations f5 2 and the like refer to standard 19 20 21 22 23 24 25 26 27 28 29 30 Keyword ip104 in the gen section Keyword ip107 in the gen section Keyword ip101 in the gen section Keyword ip103 in the gen section This setting corresponds to having all of the orbital output keywords set to 1 Relevant orbital output keyword set to 2 3 4 5 or 6 in the gen section depending on the format setting chosen Relevant orbital output keyword set to 7 8 9 10 or 11 in the gen section depending on the format setting cho sen Relevant orbital output keyword set to 2 7 or 12 in the gen section depending on which orbitals are printed Relevant orbital output keyword set to 3 8 or
274. ence difficulties can be encountered when orbitals of different symmetries swap You can fix the population in each symmetry by selecting Fixed symmetry populations This option is useful when you are running calculations on different occupations of degenerate d orbitals or if you want to converge on a state that is not the ground state but can be distin guished by the occupations of orbitals of different symmetries By default the final wave function is not localized You can localize the valence orbitals after the wave function is computed with either the Boys procedure 49 or the Pipek Mezey procedure 50 by choosing from the Final localization option menu The Boys procedure localizes the doubly occupied orbitals by maximizing the term 2 K ilrlp p Arie as Pipek Mezey localization is performed by maximizing the sum of the squares of the atomic Mulliken populations for each atom and occupied orbital See Section 6 6 on page 139 to find out how to print the localized orbitals resulting from either method Both of the available localization methods scale as N with basis set size However the use of molecular symmetry is turned off for the entire job whenever you perform a final localization so for fastest results you might want to run a job without localization then restart the job after turning on localization in the new input file See Section 7 5 on page 150 for information on restart files and restarting jobs 4 9 Solvati
275. ene started on elham schrodinger com at Thu Jan 6 10 57 33 2005 jobid elham 0 41dd8ald Jaguar version 6 0 release 9 Molecular Point Group Cl Point Group used Cl pre input checking done onee l electron integrals done hfig CHF initial guess done probe project orbitals done f grid generation done zr Monitor Detach Pause 8 Stop Kill Update i W Show jobs from current project only Update status of all jobs elham running home dya11 schrodi nger tmp tproj04138 Close Help Figure 2 7 The Monitor panel The Monitor panel is the job control panel for monitoring the progress of jobs and for pausing resuming or killing jobs All jobs that belong to your user ID can be displayed in the Monitor panel whether or not they were started from Maestro The text pane shows various output information from the monitored job such as the contents of the log file The Monitor panel opens automatically when you start a job If it is not open you can open it by choosing Monitor from the Applications menu in the Maestro main window While jobs are running the Detach Pause Resume Stop Kill and Update buttons are active When there are no jobs currently running only the Monitor and Delete buttons are active These buttons act on the selected job By default only jobs started from the current project are shown To show other jobs deselect Show jobs from current project only When a monitored job ends
276. ener ated by any unitary transformation of the canonical orbitals For LMP2 we use Boys localized 49 orbitals for which the term YgKolr o jnle jr is maximized The local virtual space for each atom is defined by orthogonalizing its atomic basis functions against the local ized molecular orbitals The correlating orbitals included in the local virtual space are thus mostly near the atom itself but because of the orthogonalization procedure they are not partic ularly well localized The Jaguar LMP2 program uses Pulay s method 46 47 48 to expand the first order wave function correction VW as a linear combination of determinants formed by exciting electrons from localized orbitals i and j to local virtual space correlation orbitals p and q 1 ws ya 14 izj pd For local MP2 we must iteratively solve the following equation which has been derived in detail by Pulay and Szebo for the coefficients C D T K FC S SC F 15 S X Fa FyCa S 0 k Here F is the Fock matrix S is the overlap matrix and T is the residual matrix defined by this equation The exchange matrix K is restricted to the dimensions of the virtual space corre sponding to the occupied localized molecular orbitals i and j The simplest updating scheme for the coefficients is to obtain updated coefficients C if iteratively from the equation Jaguar 6 0 User Manual Chapter 8 Theory Pq Pas _ pd ij Cy i Cy EG ROME g 16 De jo q where
277. energies and for prediction of enthalpy and entropy Other scale factors may be available in the literature Table 4 4 Recommended frequency scale factors for various combinations of SCF method and basis set taken from Ref 64 SCF Method Basis Set Scale Factor HF 3 21G 0 9085 HF 6 31G 0 8953 HF 6 31 G 0 8970 HF 6 31G 0 8992 HF 6 311G 0 9051 MP2 6 31G 0 9434 MP2 6 31G 0 9370 MP2 6 311G 0 9496 BLYP 6 31G 0 9945 BP86 6 31G 0 9914 B3LYP 6 31G 0 9614 B3P86 6 31G 0 9558 B3PW91 6 31G 0 9573 85 Keyword isqm 1 in the gen section 86 Keyword isqm 0 in the gen section 87 Keyword scalfr in the gen section Jaguar 6 0 User Manual 81 Chapter 4 Options 82 4 11 4 Animation of Frequencies Maestro can display vibrational animations based on Jaguar frequency data This data is written in a file with a vib extension when you perform a frequency calculation For calcula tions that use a Project Table entry as the source of input the vibrational data is incorporated when the job finishes and a Vib column is added to the Project Table The Vib column has a button labeled V for each entry that has vibrational data much like the Surf column has for surface data Clicking the button opens the Vibration panel in which you can select the frequency to be animated and control the amplitude and speed of the animation You can switch modes and change entries during the animation If the frequency job was no
278. eopt and nude Sometimes you might want a path to include a command of more than one word for instance you might want to use the UNIX command mv old filename new filename to rename a file In that case you can enter the path section in such a way that each line contains a single command To enter the path this way you must include the word line after the amp path or path label at the beginning of the path section 9 17 NBO Sections To request a Natural Bond Orbital NBO analysis at the end of the Jaguar job include an nbo section in your input file If the section is empty as it is here amp nbo amp Jaguar 6 0 User Manual 241 Chapter 9 The Jaguar Input File 242 a default NBO analysis is performed Options for NBO calculations that are specified in the NBO keylist can be included in the nbo section in the format required by the NBO program Likewise if you want to specify options for the CORE CHOOSE or NRTSTR keylists you should include them in core choose and nrtstr sections in the Jaguar input file The informa tion in all these sections is copied unchanged into NBO keylists of the same name and passed to the NBO program Jaguar s interface to NBO 5 0 does not support the DEL keylist which means that Natural Energy Decomposition Analysis NEDA is not supported The DELH keylist is also not supported If you sets nboden 1 and mp2 3 in the gen section the LMP2 density is used in the NBO analy
279. equency Related Keywords eese 199 9 5 15 Basis Set Keywords anne aan ann 200 9 5 16 Keywords Tor SCF Melligds nase 201 9 5 17 Initial Guess KEV WOES a iuste reso estet in ase GAEEERR DAP EEE RIP FAR EUN FAP FINUM 206 9 5 18 Localization Keywords entia rete ciini thea tits tane 208 9 5 19 File Format Conversion Keywords 5 irre rnt rris recta 209 9 5 20 Standard Ouftput Keywards isses 212 9 5 21 File Output Keywerds san nennen area une 214 9 5 22 Output Keywords for Each Iteration esee 215 9 5 23 Orbital Output KeyWO dS nie 215 9 5 24 Grid and Dealiasing Function Keywords sese 218 9 5 25 Memory Use Keywords titt rati eti t beilo id e tc be lode aaia 219 9 5 26 Plotting KeyWords une eue 222 9 6 The GV Section see 224 9 7 The Imp 2 Section een 225 9 8 Th amp atomie Section iei roe een 226 9 8 1 General Format of the atomic Section esse 226 9 8 2 Keywords That Specify Physical Properties unnsrssnnsnnennnnsnnnnneennnnnen 228 9 8 3 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms 229 9 8 4 Deining ETSI eH Ss scies ipie FARE eua AX RATE APO Mar ee 233 9 9 The NESS Section ee an ae 234 9 10 The guess Section dene ie 235 9 11 The pointch Section ie eee Kran 236 9 12 Th efields Section u ne een 237 9 13 The ham Section eie oett m tcc t ee
280. equested higher order moments and the corresponding traceless higher order moment tensors For example here is the output for a calculation of water s dipole and quadrupole moments Moments from quantum mechanical wave function Dipole Moments Debye X 0 0000 Y 2 1470 Z 0 0000 Tot 2 1470 Quadrupole Moments Debye Ang XX 4 0828 YY 5 7670 WE 7 1340 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole Moments Debye Ang XX YY 1 6843 222 XX YY 4 4182 XY 0 0000 XZ 0 0000 YZ 0 0000 Jaguar 6 0 User Manual Chapter 6 Output If electrostatic potential charge fitting to atomic centers is performed the output lists the number of grid points from the charge grid which is used for the charge fit It then describes the constraint or constraints for the fit followed by the calculated atomic charges and their sum The root mean square error of the charge fitting is also reported this error is calculated from examining the Coulomb field at each grid point that would result from the fitted charges and comparing it to the actual field If electrostatic potential fitting to atomic centers and bond midpoints is performed the bond midpoints are treated as dummy atoms and their descriptions and coordinates are provided before the grid points information The bond charges from the fit are provided with the label bond along with those on the atomic centers An example for water follows dummy atom x4 is between 2 and 1 dumm
281. er for adjusting Delete adjustments Clear Workspace Clear all atoms from the Workspace Enhance depth cues Optimize fogging and other depth cues based on what is in the Workspace Chapter 2 Introduction to Maestro Rotate around X axis by 90 degrees Rotate the Workspace contents around the X axis by 90 degrees Tile entries Arrange entries in a rectangular grid in the Workspace Save view Save the current view of the Workspace orientation location and zoom Display only selected atoms Choose an object type for displaying Click to select atoms to display Double click to display all atoms Also display Choose a predefined atom category Open the Atom Selection dialog box Display residues within N angstroms of currently displayed atoms Choose a radius Open a dialog box to set a value Draw bonds in wire Choose an object type for drawing bonds in wire representation Open the Atom Selection dialog box Click to select atoms for representation Double click to apply to all atoms Draw atoms in Ball amp Stick Choose an object type for drawing bonds in Ball amp Stick representation Open the Atom Selection dialog box Click to select atoms for representation Double click to apply to all atoms Color all atoms by scheme Choose a predefined color scheme Label atoms Choose a predefined label type Delete labels u D ot 5 0s
282. es 1 Molecule Theory scr Properties Solvation Output Properties select to edit options Calculate Property Surfaces MO density potential lt x Atomic el ectrostati c potenti al charges ESP Mulliken populations NBO analysis Multipole moments Polarizability Hyperpolarizability NMR Shielding Constants Electrostatic potential charges ESP Constraints Total charge only Grid type Fit ESP to Atom centers r Spherical v Rectangular spacing 0 75 koh Start Read Write Edit Reset Close Help Figure 4 7 The Properties folder showing controls for ESP charges If both electrostatic potential fitting and multipole moment calculations are performed the moments are also computed from the fitted charges for purposes of comparison The electrostatic potential is itself computed on a grid By default this grid has the same form as the other pseudospectral grids it is formed by merging sets of spherical shells whose grid points are centered on each nucleus The Spherical option is selected by default in the Grid type section An alternative is to use a regular lattice of grid points 59 by choosing Rectangular in the Grid type section You can then set the spacing in bohr between points in this lattice in the text box For either grid type points within the molecular van der Waals surface are
283. ese sets is a free format table The first row of the table lists the keywords whose values are to be set for each atom This row is the column heading row Subsequent rows list the values for the keywords for each relevant atom For instance in the following atomic section amp atomic atom mass vdw2 Hl 2 00 1 20 H2 2 00 1 20 atom vdw2 Oo 1 55 amp the keywords are atom the atom label or number mass the nuclear mass in amu and vdw2 the van der Waals radii for solvation and the lines for the atoms H1 and H2 specify that these atoms have a nuclear mass of 2 00 amu deuterium and solvation van der Waals radii of 1 2 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File while the line for atom O specifies a solvation van der Waals radius of 1 55 for this atom It is not necessary to list information for atoms that are to be treated in the default manner Keywords are case insensitive Columns can be given in any order All entries in a row should be separated by one or more spaces or tabs but columns do not need to be aligned The atom column must be included in every set of atomic input values The atom identifiers can be either atom labels such as H1 or O in the example above or atom index numbers such as 2 for the second atom listed in the zmat input Atom label input is case sensitive If you do not want to set a value for a given atom you can use a or to indicate that the default value
284. esian file mopint Mopac Internal file mopout Mopac Output file pemod PC Model file pdb PDB file psin PS GVB Input file psout PS GVB Output file msf Quanta MSF file schakal Schakal file shelx ShelX file smiles SMILES file spar Spartan file semi Spartan Semi Empirical file spmm Spartan Molecular Mechanics file mol Sybyl Mol file mol2 Sybyl Mol file wiz Conjure file unixyz UniChem XYZ file XYZ XYZ file xed XED file 280 Jaguar 6 0 User Manual Chapter 11 Running Jobs Note that the format keywords are not used for file extensions as they are when you use the babel and babelg keywords in a Jaguar input file The input and output file names given in the jaguar babel command are used as they are If you omit the output file name or if you give CON as the output file name the output is written to standard output You can add hydrogen atoms to a structure when you do a conversion using the h option and you can delete hydrogen atoms from a structure using the d option Babel can convert multi structure files to other multi structure files or to a set of single struc ture files You must supply both an input file name and an output file name if you are converting a multi structure file You can select the structures to convert by specifying the range input argument A valid ranges is in the form numberl number2 or the word all to select all structures The quotes are required For Jaguar output files the last structure is con
285. et perturbation theory calculation cis Performs CI singles calculation derla Calculate analytic one and two electron first derivatives derib lmp2der Calculate analytic one and two electron first derivative terms for LMP2 wave lmp2gda functions lmp2gdb nude Calculates numerical second derivatives of energy as numerical derivatives of the analytical gradient freq Calculates vibrational frequencies and related properties ira irb Calculate dipole derivative terms needed for calculation of IR intensities geopt Performs geometry optimization pbf Solves Poisson Boltzmann equations for solvation calculation solv Performs solvation calculation using results from Jaguar Poisson Boltzmann solver sole Checks solvation energy convergence dsolv Computes solvation related gradient terms for solvated geometry optimizations post Processes files output etc at end of run timex Checks CPU time for entire run machid Utility program returns machine information note not used in Jaguar calcula tions Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File The simplest form available for the path section is a list of the programs to be run as in the following example amp path pre hfig grid rwr amp It is not actually necessary to list pre in paths since the pre program will always be run If you want to run additional programs after a standard Jaguar calculation you can use the Word path to indicate the default path a
286. etry optimization then restart the calcula tion using the HF results in an LMP2 geometry optimization See Section 7 5 for a description of restarting calculations and incorporating previous results in a later run Whenever you are doing a geometry optimization make sure that you really do obtain a converged structure the run ends before converging if you reach the maximum number of iter ations allowed as set in the Optimization folder If it did not reach convergence you can restart the run as described in Section 7 5 Jaguar 6 0 User Manual 149 Chapter 7 Using Jaguar 150 7 4 Setting Up GVB Calculations For most molecules Lewis dot structures give a reasonable idea of what GVB pairs you should consider setting If you want to automatically assign pairs by Lewis dot structure for input files generated and submitted outside the GUI see Section 9 5 5 on page 176 You do not have to assign all possible GVB pairs You can set GVB pairs in any order If you are studying a dissociating bond you should assign all reasonable GVB pairs for that bond For some purposes such as for dipole moment calculations you may find that assigning only pairs for bonds between two different atoms is sufficient Bonds to hydrogen atoms can also be ignored for some cases You should not assign GVB lone pairs if you are using a minimal basis set since the basis set does not have enough degrees of freedom to handle the lone pair When assignin
287. ettings If you are working from the GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI 6 1 Summarizing Jaguar Results You can obtain summaries of Jaguar results in simple table form by using the following command jaguar results option list output file list Jaguar searches the output files you specify for the information you request through the command options The order of the options determines the order in which the corresponding data is printed The options are listed in Table 6 1 grouped into classes You can also obtain a list of supported options by entering the command jaguar results help The tables produced by jaguar results can describe results from one job or several jobs The results can be restricted to final results from each job listed the default or can include inter mediate results SCF energies for each geometry in an optimization for instance By default each line lists information that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure Each of these types of Jaguar 6 0 User Manual 105 Chapter 6 Output results tables are described below Data values for each output file are printed with results for each job on a separate line Table 6 1 Options for the jaguar results command Option Meaning Job and molecular information opti
288. etween 0 and 0 5 to pick a guess closer to the product geometry set the Initial LST guess value to a number between 0 5 and 1 0 19 Keyword qstinit in the gen section Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans For the first few steps of a QST guided search the optimizer is restricted to searching along the circular curve connecting the reactant transition state guess and product structures This restriction prevents the optimizer from being led far astray by the inaccuracies of the guess Hessian and prevents it from exploring transition states that do not correspond to the reaction of interest During these steps the optimizer approaches the maximum energy structure along the reactant to product curve and also greatly improves the Hessian Once it has obtained the improved Hessian and transition state guess the optimizer removes the requirement that the search must be along the curve between the structures For all subse quent steps in the search the optimizer follows the Hessian eigenvector that is most similar to the tangent of the circular curve If no Hessian eigenvector is sufficiently similar to the tangent to the curve the optimizer follows the lowest eigenvector If you have a fairly good transition state guess but cannot provide reactant or product struc tures you can still use the standard non QST method This optimizer attempts at each step to maximize the energy along the lowest frequency eigenve
289. exchange energies and their sum are listed Finally a table of GVB pair information is given Here is an example of this GVB infor mation in the SCF output for a water molecule with two GVB sigma pairs Total Coulomb Exchange Total two electron terms 37 90378136033 46 96140169504 9 05762033471 Hamiltonian 1 25 77166631229 32 84704880440 7 07538249211 Hamiltonian 2 6 02807668738 6 99023521309 0 96215852571 Hamiltonian 3 6 02990515066 6 99271668375 0 96281153309 Hamiltonian 4 0 03711925295 0 06576591758 0 02864666463 Hamiltonian 5 0 03701395705 0 06563507622 0 02862111917 List of Intra Pair K Energies 0 03983705429 0 03981442075 Sum of Intra Pair K Energy 0 07965147505 GVB pair information first natural orbital second natural orbital orb ham shl 1 4 2 2 0 995433818 6 4 4 0 095454256 0 824997160 0 020103338 2 5 3 3 0 995443725 7 5 5 0 095350881 0 825171705 0 020091467 ci energy pair orb ham shl ci coeff ci coeff overlap lowering SCFE SCF energy GVB 76 06328826029 hartrees iterations 8 Jaguar 6 0 User Manual Chapter 6 Output Each row in the GVB pair information table lists the pair number the orbital number after all core and open orbitals have been assigned numbers Hamiltonian number after the core Hamiltonian and any open Hamiltonians have been assigned numbers and shell number after the core shell and any open shell have been assign
290. ey started If frozen Cartesian coordinates are included in the input for an optimization Jaguar uses Carte sian coordinates for the optimization rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry 3 4 4 Z Matrix Format for Geometry Input Like Cartesian geometries Z matrix format geometries also specify atoms by atom labels that begin with the one or two letter element symbol The atom label is case insensitive The element symbol may be followed by additional characters as long as the atom label has eight or fewer characters and the element symbol is still clear The first line of the Z matrix should contain only one item the atom label for the first atom For example N1 This atom is placed at the origin The second line contains the atom label for atom 2 the iden tifier of atom 1 and the distance between atoms 1 and 2 Identifiers can either be atom labels or atom numbers the position in the list 1 for the first atom 5 for the fifth atom listed and so on In this example the identifier for the first atom could be either N1 or 1 The second atom is placed along the positive z axis For example N1 C2 N1 1 4589 Jaguar 6 0 User Manual 37 Chapter 3 Running Jaguar From Maestro 38 places the carbon atom C2 at 0 0 0 0 1 4589 in Cartesian coordinates Distances between atoms must be positive The third line is made up of five
291. force symmetry in either Z matrix coordinates or Cartesian coordinates 5 2 4 Freezing Specific Coordinates To constrain specific coordinates to their original values during an optimization you can use the controls in the Add New Constraint section of the Optimization folder or you can edit the input file The Edit Job dialog box provides a convenient way of editing the input file Using the Add New Constraint section of the Optimization folder see Figure 5 1 on page 88 you can pick atoms in the Workspace to define the coordinates to freeze First choose the coor dinate type Angle Cartesian Dihedral or Distance from the Type option menu then choose Atoms or Bonds from the Pick option menu then pick the required number of atoms or bonds in the Workspace to define the coordinate The coordinate and its type are listed in the Constraints table If you choose Cartesian you can choose which combination of coordinates x y or z to freeze from the Constrain in option menu For protein dihedral angles you can also select one of the standard angles by clicking Select and selecting the desired angle When you define constraints in this way internal coordinates are added to a coord section with a sign to indicate that the coordinate is frozen and Cartesian coordinate constraints are added to the zmat section by adding a sign after the constrained coordinates This means that the zmat section must be in the right format for the cons
292. format keywords are listed in Table 11 5 Table 11 5 Input format keywords and file types for babel file format conversions Format Keyword File Type alc Alchemy file prep AMBER PREP file bs Ball and Stick file bef MSI BGF file Jaguar 6 0 User Manual Chapter 11 Running Jobs Table 11 5 Input format keywords and file types for babel file format conversions Continued Format Keyword File Type car boog caccrt cadpac charmm c3dl c3d2 cssr fdat gstat dock dpdb feat fract gamout gzmat gauout g94 gr96A gr96N hin sdf jagin jagout m3d macmol macmod micro Biosym CAR file Boogie file Cacao Cartesian file Cambridge CADPAC file CHARM m file Chem3D Cartesian 1 file Chem3D Cartesian 2 file CSD CSSR file CSD FDAT file CSD GSTAT file Dock Database file Dock PDB file Feature file Free Form Fractional file GAMESS Output file Gaussian Z Matrix file Gaussian 92 Output file Gaussian 94 Output file GROMOS96 A file GROMOS96 nm file Hyperchem HIN file MDL Isis SDF file Jaguar Input file Jaguar Output file M3D file Mac Molecule file Macromodel file Micro World file Jaguar 6 0 User Manual 279 Chapter 11 Running Jobs Table 11 5 Input format keywords and file types for babel file format conversions Continued Format Keyword File Type mm2in MM2 Input file mm2out MM2 Output file mm3 MM3 file mmads MMADS file mdl MDL MOL file file molen MOLIN file mopert Mopac Cart
293. g Jaguar NBO 5 0 6 3 8 Frequency IR Intensity and Thermochemistry Output If you calculate vibrational frequencies any SCF calculations during the run use the RMS density change convergence criterion described in Section 4 8 on page 68 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations do To compute the Hessian for vibrational frequencies Jaguar calculates the second derivatives either analytically or numerically as the derivatives of the analytical first derivatives depending on the type of calculation see Section 4 11 on page 79 for details Whenever numerical second derivatives are computed after an SCF calculation whether for frequency output for an initial Hessian or for updating during geometry optimization the programs nude onee hfig grid rwr scf der1a rwr and der1b run setting up and performing SCF calculations and evaluating analytic gradients at 6N tom perturbed geometries unless the number of perturbed geometries needed is reduced by the use of molecular symmetry After the calculations at the perturbed geometry Jaguar performs one final calculation at the unper turbed geometry The Jaguar programs run may vary slightly for non HF calculations as described earlier in this section After the data from all perturbed geometries is collected the program nude prints the numerical first derivatives
294. g directory When you read a Jaguar input file you can read the geometry only or you can read the entire input file To read just the geometry choose Geometry only from the Read as option menu To read the entire input file choose Geometry and settings from the Read as option menu If you read in a geometry only from a file Jaguar also tries to obtain information on the molecular charge If you read the geometry and settings the settings are used to determine the Jaguar task which might not be the task with which you opened the Jaguar panel For example if you chose Single Point Energy then read an input file for a geometry optimization including the settings the task is reset to Optimization The structures in the input file are added as entries in the Project Table named with the stem of the input file name by default For example reading h2o in creates an entry named h2o Jaguar 6 0 User Manual 41 Chapter 3 Running Jaguar From Maestro 42 Jaguar Read Sei Filter zonel dyall jaguar ini Directories dyall jaguar dyall jaguar ERN 17 FE Launch Directory Working Directory Read as Geometry and settings Selection zonel dyall jaguar T Figure 3 3 The Jaguar Read dialog box To read geometries from files generated or used by other programs you must import them into Maestro using the Import panel The files are imported using the file format conversion progra
295. g lone pairs you should only put one GVB lone pair on atoms from the nitrogen group two for those from the oxygen group three for the fluorine group and one for the carbon group In the last case assigning lone pairs is only reasonable when the atom is bonded to only two neighbors If you assign one GVB lone pair for an atom you should also assign any other possible GVB lone pairs on that atom 7 5 Restarting Jobs and Using Previous Results Sometimes you may find it useful to restart a job either because you want to refine the results and do not want to start from the beginning of the calculation because you want to alter the calculation slightly but want to use an initial guess or geometry from the previous run or because you encountered some sort of problem that prevented the job from finishing New input files which are also called restart files generated during each job can be used to restart the jobs These files are automatically written to your local job directory at the end of a run if the run did not finish you can usually find the new input file by following the directions at the end of this section The restart file contains all the information needed for a new run incorporating the results from the first run This file contains the same job settings you made for the original input file for the job but also contains the results of the job the final wave function the final geometry and the like Thus if you want to restar
296. ge 46 Read Opens a file browser for selecting a Jaguar input file to read in See Section 3 5 on page 41 Write Opens a file browser for writing the current geometry and settings in the Jaguar panel as an input file or for writing the current settings as a batch script Edit Opens the Edit Job dialog box in which you can edit the contents of the input file that Maestro is constructing Any changes you make in this dialog box are reflected in the settings in the Jaguar panel You can also add keywords that are not available as GUI set tings see the next section Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro 34 Reset Resets all the settings in the Jaguar panel to the default state for the selected task Close Closes the Jaguar panel Help Opens the help viewer at the topic for the currently displayed folder 3 3 The Edit Job Dialog Box While most of the common settings for Jaguar jobs can be made in the Jaguar panel you might need to make changes to the settings add keywords to the input file for options that are not available from the Jaguar panel or make changes to the geometry You can make these changes in the Edit Job dialog box which you open by clicking Edit in the Jaguar panel Apart from standard editing tools this dialog box has special tools for editing Jaguar input files The basic editing tools are contained in the File and Edit menus The File menu allows you to save the
297. ght differ from the error messages described here depending on your hardware and X implementation Remember that your X server is either your workstation or the machine that acts as the server for your X terminal the display host is the workstation or terminal at which you are sitting and you are trying to start Jaguar as an X client on some machine not necessarily serving as your X server Some of the issues addressed here are standard X windows or UNIX issues and consulting your X and UNIX documentation may help Also you may be able to avoid repeatedly entering commands described in this section by including them in your login cshrc or other startup files in your home directory If you can start Maestro but you have problems submitting jobs skip to Section 12 1 4 on page 292 and Section 12 1 5 on page 293 12 1 4 The SCHRODINGER Environment Variable Before running Jaguar on any particular machine you must set the environment variable SCHRODINGER to point to the installation directory on that machine This is the directory Jaguar 6 0 User Manual 289 Chapter 12 Troubleshooting 290 containing Jaguar version 6 0 which is in a subdirectory called jaguar vxxxxx where xxxxx is the five digit version number To check whether the SCHRODINGER environment variable is set enter the command echo SCHRODINGER If the output from this command is a directory containing Jaguar you can skip the rest of this subsect
298. guar Run Batch File Script zone2 0B builds r2004 Browse Source of structures Selected structure files Files zone1 dyall jaguar alc Browse For input files Use structure only ignore settings v Use both structure and settings Start Close Help Figure 3 8 The Run Batch File panel Jaguar batch jobs can be run from the Run Batch File panel which you open by choosing Run Batch File from the Jaguar submenu of the Applications menu To run a batch job you must select a script select a source of structures and start the job If you choose to read Jaguar input files for the structural input you can choose whether to use or ignore the settings in the input files To select a script you can enter the path in the Script text box or click Browse and choose a script in the Select Batch Script panel This panel is a file selector with the usual file browsing tools a Filter text box a Directories list a Files list and a Selection text box By default infor mation is displayed in the lists and the filter for the current working directory To select one of the supplied Jaguar scripts click Jaguar Scripts in the Directory section then select the script When you select a script the Notes text area shows comments from the batch script When you have chosen the directory choose a script from the list of scripts then click OK The built in scripts are described briefly in Table 3 1 Table 3 1 Descriptio
299. guar This string should be dafv followed immediately by four digits giving the version number times 100 Lead zeros are added if necessary The second line has two integers The first integer gives the number of dealiasing function sets provided for each atom type each set is used for a particular grid during the calculation The ordering of the sets used for each grid type is determined by the parameters named dcoarse dmedium and so on which are specified in the gen section of the input file By default the coarse grid is listed first then the medium fine ultrafine and gradient grids in that order The second number in the second line gives the number of ranges described in each of these dealiasing function sets The ranges correspond to particular RwR blocks for the calculation One of these ranges is the long range basically covering the whole molecule another is the home atom range which actually only includes the relevant atom itself and the rest are increasingly large neighbor ranges The number of ranges should currently not exceed 10 The sample file s second line indicates that for each basis set five dealiasing function sets are spec ified for each atom and that each of these sets contains dealiasing functions for a total of six ranges the long range functions the functions for the home atom and the functions for four other neighbor ranges 1 To see this connectivity information for a system set ip12 2 in the gen
300. guar input file and how to use it to run Jaguar from the command line You might want to run Jaguar from the command line in order to submit a job at a later time when computers are less busy to use batch scripts to run multiple jobs in succession to submit jobs from a non X terminal or to automate job submission with input files created by using other programs or by creating and editing input files yourself The sections in this chapter discuss the Jaguar input file format describing the general file format first then describing each section of the input file starting with the geometry input zmat and the keyword gen sections In the tables of this chapter default values of keywords are set in bold italic 9 1 General Description of the Input File The input file often begins with an optional line indicating the version number of Jaguar such as v60012 The other parts of the input file are either single lines composed of options in capital letters followed by arguments on the same line sections describing the molecule and the calculation whose formats will be described later in this chapter or comments 9 1 1 Input File Format The input file should have the following format where square brackets denote optional entries and entries in italics represent a character string with no spaces comments sections describing molecule amp calculation BASISFILE file path name basis ATOMIGFILE file path name atomig DAFFILE fi
301. h the rest of your input for instance the basis set could be missing basis functions for some atom or atoms in your molecule Basis sets that do not have pseudospectral grids and dealiasing functions are listed in italics in the Basis Set option menu If you do not choose a basis set for a calculation Jaguar uses the 6 31G basis set if 6 31G basis functions are available for all atoms in the input and otherwise uses the LACVP basis set by default These basis sets are described in more detail below The Polarization option menu provides the choices none and In general the option places polarization functions on all atoms except for transition metals and the option places polarization functions on all atoms except for transition metals H and He The tables below describe in detail the atoms that have polarization functions in each basis set The correlation consistent basis sets cc pVnZ are intrinsically polarized The Diffuse option menu provides the choices and The option places diffuse functions on all atoms while the option places diffuse functions on all atoms except H and He Diffuse functions are useful for calculations on van der Waals complexes or molecules that include atoms with negative charges For the basis set that you select a message giving the number of functions and stating whether pseudospectral grids are available and whether ECPs are used is displayed below the controls Table 4 1 lis
302. h tcsh setenv MP HOSTFILE home userid my hostfile sh ksh bash export MP HOSTFILE home userid my hostfile If you are unsure of your system configuration contact your system administrator Ensure that the schrodinger hosts file is properly configured for your cluster See Section 11 1 4 on page 272 for more information on this file Finally you must also make sure you have rsh access to the host even if you are on it To do this add a line to your rhosts file that specifies the node that you need access to and your login name bobcat schrodinger com userid This gives user userid rsh access to host bobcat schrodinger com Jaguar 6 0 User Manual 305 Chapter 13 Parallel Jaguar 306 13 2 Running Jobs in Parallel To run Jaguar jobs in parallel you need only specify the number of processors to use for the job at the time you launch it You do not need to launch mpirun or poe this is done automati cally by Jaguar If you launch the job from the command line set the PROCS option to the number of processors to be used For example jaguar run PROCS 8 HOST mysmp jobname If you launch the job from the GUI type the number of processors to be used into the of Processors window in the Jaguar Run panel By default the maximum number of processors that you can request is shown in this window The number is read from the processors line for the selected host in the schrodinger hosts file If you need t
303. h the electrostatic potential was evaluated The cartesian coordinates of the atoms in bohrs are given next one atom per line Each subsequent line contains information for one grid point the electrostatic potential value in hartrees the coordinates of the grid point in bohrs and if ip172 3 the grid weights 9 5 22 Output Keywords for Each Iteration The information in Table 9 34 concerns output which can be printed out every SCF iteration if the keyword is set to 2 The information is not printed if the keyword is set to 1 The option ip152 is the only one whose default value of 1 indicates that it is on When ip152 is set to 1 the file restart in is created in the temp directory for the job at the end of the last completed iteration overwriting the restart in file created from the previous iteration This input file can then be used to restart the calculation To turn off ip152 you must set it to 0 9 5 23 Orbital Output Keywords Orbital information can be printed out as well The orbital keywords determine what orbitals are printed in the output at what stage they are printed and the format Jaguar 6 0 User Manual 215 Chapter 9 The Jaguar Input File 216 Table 9 34 Effect of setting output keywords for each iteration to 2 Keyword Description of What Is Printed When ipi 2 ip15 DUS coefficients ip17 Energy components ip110 Density matrix if Fock matrix updating was not performed during that iteration
304. he Applications menu The Jaguar panel opens with the folders that are relevant to the chosen coordinate scan type After you have made settings in the other folders you can set up the coordinates and their values in the Scan folder Coordinates can be added to the scan using the Add New Coordinate section and picking atoms or bonds in the Workspace To set up a coordinate first choose a coordinate type from the Type option menu The allowed coordinate types and the number of atoms to pick for each are Jaguar 6 0 User Manual 99 Chapter 5 Optimizations and Scans 100 Cartesian X X coordinate of an atom Pick one atom Cartesian Y Y coordinate of an atom Pick one atom Cartesian Z Z coordinate of an atom Pick one atom Distance Distance between two atoms Pick two atoms or one bond Angle Angle between three atoms Pick three atoms or two bonds Dihedral Dihedral angle between four atoms Pick four atoms or three bonds When you have chosen a coordinate type select Pick and choose an object from the Pick option menu You can pick Atom for Cartesian coordinates and Atom and Bond for all other types of coordinates If you pick atoms for a distance angle or dihedral they need not be bonded to each other The atoms are marked in the Workspace as you pick them and each coordinate is marked in the Workspace and entered in the Defined coordinates table as it is completed The Defined coordinates table displays information on th
305. he Help panel is displayed with a rele vant help topic For help with a concept or action not associated with a panel open the Help panel from the Help menu or press CTRL H If you do not find the information you need in the Maestro help system check the following sources The Maestro User Manual The Frequently Asked Questions page found at http www schrodinger com Support fag html You can also contact Schr dinger by e mail or phone for help e E mail help schrodinger com Phone 503 299 1150 2 12 Ending a Maestro Session To end a Maestro session choose Quit from the Maestro menu To save a log file with a record of all operations performed in the current session click Quit save log file in the Quit panel This information can be useful to Schr dinger support staff when responding to any problem you report Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro The Maestro interface to Jaguar can simplify the preparation and submission of jobs You can run Maestro on one machine display it to another and start a Jaguar calculation on yet another machine The main part of the interface is the Jaguar panel which you use to prepare job input Without the Jaguar panel you would have to create input files with particular formats in order to run Jaguar Maestro creates these input files for you based on information you provide and submits the job This frees you from learning the input format an
306. he maximum difference in energy between one SCF iteration and the next required for convergence and dconv the criterion for the root mean square change in density matrix elements The default value of econv is normally 5 0x10 hartrees However for polarizability or hyperpolarizability calculations econv is 1 0x10 hartrees by default When the root mean squared change in density matrix elements for a polarizability hyperpolarizability or geometry optimization calculation is less than dconv whose default value is 5 0x10 the calculation is considered to have converged By default calculations use the DIIS or GVB DIIS convergence scheme which generates an estimate of the Fock matrix that is a linear combination of current and previous Fock matrices determined to minimize the norm of the error vector The keyword maxdiis sets the maximum number of Fock matrices default 10 that are used for this scheme during any iteration The keyword stdiis gives an error criterion DIIS is started when the largest value of the DIIS error vector is less than the value of stdiis hartrees which is 100 0 by default In general after Jaguar 6 0 User Manual 201 Chapter 9 The Jaguar Input File 202 GVB DIIS starts any density matrix averaging requested by the keywords iteravg and istavg explained in Table 9 28 is turned off The keyword vshift sets the amount the virtual orbital energies are increased before diagonal ization in atomic un
307. he same fragment You can then request that all the atoms in one frag ment be treated as dummy atoms or counterpoise atoms or used as the only atoms for which numerical frequencies will be calculated where Hessian elements for other atoms are zero The default frag value for each atom is 0 meaning it is not considered part of any fragment To assign a group of atoms to the same fragment in the frag column of the atomic section enter the same value for each atom To treat all atoms in a fragment as counterpoise atoms set icpfrag fragno in the gen section of the input file where fragno is the integer fragment label from the frag column of the atomic section To treat them all as dummy atoms make the keyword setting idelfrag fragno in the Jaguar 6 0 User Manual 233 Chapter 9 The Jaguar Input File 234 gen section To compute partial frequencies for a particular fragment make the setting fregfrag fragno in the gen section of a frequency input file One further use of fragments is for antiferromagnetic systems for which standard transition metal initial guesses do not work For an antiferromagnetic system containing two metal atoms that are not bonded you can use a 2spin column to set up the initial guess When the metals are within bonding distance or when there are more than two metals you should set iopt420 420 in the gen section then manually assign ALL atoms to fragments using the frag column of the atomic section The
308. hybrids you need to specify a Slater or Xo local exchange functional a non local exchange functional a local correlation functional and a non local correlation func tional i e j k I and m must all be non zero if i is 2 Even when you use the Lee Yang Parr functional in a Becke 3 parameter hybrid you must list a purely local correlation functional which will be used to adjust the local correlation contribution For Becke 3 parameter hybrids Jaguar 6 0 User Manual 183 Chapter 9 The Jaguar Input File 184 that do not include the Lee Yang Parr functional the coefficients of the exact HF exchange and of the local exchange non local exchange local correlation and non local correlation func tionals are 0 2 0 8 0 72 1 0 and 0 81 respectively If the Lee Yang Parr functional is used in a Becke 3 parameter hybrid its coefficient is 0 81 and the coefficient of the local correlation functional used is 0 19 If idft 1 the values of the keywords xhf xexl1 xexl9 and xexnln determine the contribu tions of the exact exchange and the exchange functionals while the keywords xcorln and xcornln control the contributions of the correlation functionals as listed in Table 9 15 For example with idft 1 xhf 0 332 xexl1 0 575 and xcorl1 0 575 and with all other xex and xcor keywords set to zero the exchange is treated with a combination of the exact exchange and the Slater local functional while the correlation functional
309. ial fitting when the grid keyword gcharge 2 Similarly the keyword denspc is used to set the spacing of the electron density rectangular grid when Idens 1 and the grid keyword geldens 3 The efield keyword allows you to specify an electric field for finite field polarizability and hyperpolarizability calcula tions The default value shown in Table 9 25 applies when ipolar gt 1 For ipolar 1 3 point polarizability only calculations the default value is 0 006 au If you want to print out the electrostatic potential at grid points that you specify add the keyword settings gcharge 6 and ip172 2 to the gen section of your input file The gcharge 6 setting instructs Jaguar to use the grid points and weighting factors in a file whose name and location are specified by the GPTSFILE line in the input file see Section 9 1 on page 167 The ip172 2 setting instructs Jaguar to write out a file named jobname resp containing the electrostatic potential data see the text under Table 9 33 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Gas phase NMR shielding constants are available for closed shell and unrestricted open shell wave functions To calculate chemical shifts you should calculate NMR shielding constants for the reference molecules for each element of interest in the same basis set and with the same method as for the molecule of interest By default shieldings are calculated for all atoms including those with ECPs Shi
310. ical calculations for multiple conformations generated from a MacroModel solution phase conformational search and use all of this information to compute the pK Two ways of doing this are a Pick the conformer that has the lowest solution phase free energy for each protona tion state and compute the pK from this value This method is analogous to 1 above but allows for imprecision in the conformational search protocol It also takes more CPU time b Carry out a statistical mechanical average over conformations to determine the aver age pK The assumption made if this option is chosen is that the midpoint of the pK titration curve is achieved when the total population of the deprotonated state summing over all deprotonated conformations is equal to the total population of the protonated state also summing over all conformations This approach should be more accurate than that described in a although how important statistical effects are in practice remains to be ascertained 14 2 2 Equivalent Sites Some molecules have two or more equivalent sites for protonation or deprotonation Examples include ethanediamine the analogous dicarboxylic acid or the molecule melamine in our suite of test cases which has three equivalent sites In this situation there is a statistical correction factor arising from increased entropy of the appropriate species As we do not have an auto mated facility for recognizing equivalent sites in the current
311. ield UFF Because UFF includes parameters for all elements in the periodic table it can be used for inorganic complexes as well as organic compounds During the UFF minimization a status box is displayed To stop the minimization click Stop in this status box The convergence criteria for the cleanup minimization are deliberately set fairly loose so that even fairly large systems can be optimized interactively The practical size limit is about 300 atoms In addition a time limit is imposed on the minimization to keep it from running exces sively long As a result you might find that the geometry continues to change if you perform a second cleanup minimization on a cleaned up structure Jaguar 6 0 User Manual 43 Chapter 3 Running Jaguar From Maestro 44 UFF cleanup minimization is useful for quickly bringing a distorted molecule back into the neighborhood of the ab initio minimum energy geometry in preparation for full ab initio geometry optimization However it is no substitute for ab initio optimization because UFF is a relatively simple force field It is probably a good idea to perform a cleanup minimization after creating a new molecule in the Build panel On the other hand performing a cleanup minimiza tion on a molecule that has already undergone ab initio minimization is likely to move the molecule away from the ab initio minimum Also you should be careful to avoid cleaning up a structure that has been prepared as a
312. iency For the initial iterations of an optimization the SCF calcu lations are performed at the Quick accuracy level described in Section 4 8 1 on page 68 unless the input contains a transition metal in which case the accuracy level is Accurate However for the last few geometry iterations the accuracy level for the SCF calculations is reset to the Accurate level which uses tighter cutoffs and denser pseudospectral grids than the Quick level For optimizations to minimum energy structures or transition states the convergence criterion for SCF calculations is chosen to assure accurate analytic gradients For these jobs a wave function is considered converged when the root mean squared RMS change in density matrix Jaguar jaguar EIEE Use structures from Workspace included entries 1 Molecule Theory scr Optimization Properties Solvation Output Maximum steps 100 Convergence criteria Default v Loose Initial Hessian Schlegel guess 1 Coordinates Redundant internal Type Cartesian Constrain in XYZ Pick Atoms 3eeci Constraints Constraint birena Targets r Selected constraint C2 C3 C4 E iA C4 C5 C6 Ems Tange 0 0000 x W Dynamic Target value Delete Delete All Jot Start Read Write Edit Reset Close Help Figure 5 1 The Optimization folder Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans
313. ilable from the Coordinates option menu in the Optimization folder Cartesian and Z matrix Cartesian coordinates avoid the problems of collinear coordinate sets but an optimization in Cartesian coordinates is likely to take longer than one in redundant internal coordinates Using the Z matrix coordinates is the other alternative Choosing a set of Z matrix coordinates that produces an efficient optimiza tion is not a trivial task and requires an understanding of the coupling between simple internal coordinates You can mix Cartesian and Z matrix coordinates in the geometry definition zmat section but if you do you cannot use either of these two options for geometry optimizations 5 2 Constraining Coordinates When you optimize the geometry of a molecule you might want to freeze certain coordinates or constrain them to be equal to each other Freezing coordinates reduces the number of free parameters in the optimization and may reduce the number of steps to convergence or allow 9 Keyword inhess 1 in the gen section 10 Keyword inhess 0 in the gen section 11 Keyword inhess 1 in the gen section 12 Keyword inhess 4 in the gen section 13 Keyword intopt 1 in the gen section 14 Keyword intopt 0 in the gen section 15 Keyword intopt 2 in the gen section Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans you to converge a difficult optimization in stages Constraining coordinates can be used to en
314. imiza tion Transition State IRC Scan These folders are described in Chapter 5 along with other information about optimizations and scans Output options are described in Chapter 6 This chapter describes the settings that can be made in the Molecule Theory SCF Properties and Solvation folders The footnotes in this chapter indicate the Jaguar input file keywords and sections that corre spond to settings made in the GUI If you are working from the GUI you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the GUI or if you want to edit keywords directly by using the Edit Job window described in Section 3 3 on page 34 4 1 Molecule Settings The top part of the Molecule folder provides controls for the molecular charge the spin multi plicity and the application of molecular symmetry Setting charge and spin multiplicity was discussed in Section 3 6 on page 42 Briefly you can enter the charge and spin multiplicity in text boxes or you can use values that are listed in the Project Table If you choose the latter you can create the corresponding properties and enter values for them if they don t exist By default Jaguar takes advantage of molecular symmetry in order to obtain CPU savings Both Abelian and non Abelian point groups are recognized You can select whether to use the full symmetry Abelian symmetry D2h and subgroups or turn the use of symmetry off in
315. in a Jaguar calculation see Section 9 5 24 on page 218 Comments in the input file are ignored by Jaguar 9 1 2 Sections Describing the Molecule and Calculation The rest of the input file is composed of named sections The sections may appear in any order Character case upper or lower is ignored therefore either case or a combination of the two may be used Equals signs commas blank spaces and tabs are all considered spacing characters however if you plan to use the GUI we suggest that you use equals signs between a keyword and its value and avoid using them anywhere else Blank lines or multiple spacing characters in a row are equivalent to a single spacing character and thus may be used to improve readability The gen section contains a list of the general keywords which control the calculation Defaults are provided for all unspecified keywords The other sections contain lists such as atomic coordinates The sections are listed in Table 9 1 Each section has a distinct format the formats are described in detail in the rest of this chapter Keywords in the gen section can have integer real or character string values Generally valid integer values are limited to a small set which differs for each keyword Real values can optionally include a d or e floating point power of ten Character string keyword values may be limited to a small set as for a basis set descrip tion or may allow a general string
316. in a force table similar to the usual geom etry optimization force table described earlier in this section The output then lists the matrix indices of the most asymmetrical Hessian element before symmetrization The symmetrized numerical Hessian is not printed in the output but can be found in the restart file which is discussed in Section 7 5 on page 150 For either analytic or numerical frequency calculations the output from the program req contains the actual frequencies and normal modes from the computed Hessian or from the last available Hessian generally the initial Hessian guess if you used the Use available Hessian Jaguar 6 0 User Manual 129 Chapter 6 Output 130 choice to request vibrational frequencies The output from the program freq first lists the harmonic frequencies in cm and their symmetries if symmetry is on for the job then the normal modes The system s thermochemical properties the constant volume heat capacity C entropy S enthalpy H internal energy U and Gibbs free energy are then listed for the specified pressure and temperatures as well as at 0 K Here is an example of this output from a vibrational frequency calculation on FOOF Start of program freq harmonic frequencies in cm 1 reduced masses in amu force constants in mDyne A and normal modes in cartesian coordinates IR intensities in km mol frequencies 226 83 587 12 708 27 994 11 1063 07 1086 36 intensities 69 0
317. in list from the How option menu for the original run as described in Section 6 6 on page 139 and the resulting orbital output could be copied from the output file into the guess section of the input file for the next run Similarly you could set the relevant orbital output keyword to 4 5 9 or 10 in the gen section of the input file for the first run as described in Section 9 5 23 on page 215 and use the resulting output file s orbital output in the guess section of the input file for the next run A sample guess section for water with an STO 3G basis set follows The oxygen is atom 1 and for each molecular orbital coefficients for the oxygen s 1s 2s 2p 2p and 2p orbitals are input The 1s coefficient for the first hydrogen atom follows followed by the 1s coefficient for the second hydrogen amp guess basgss sto 3g 1 orbital energy 20251577D 02 99421641D 00 25847131D 01 31906711D 02 88241647D 15 26760209D 02 55838749D 02 55838749D 02 2 orbital energy 12575489D 01 23376569D 00 84444935D 00 94117884D 01 39742456D 17 78936818D 01 15559441D 00 15559441D 00 3 orbital energy 59385470D 00 30846088D 09 13714419D 08 39372414D 00 21348436D 14 46944485D 00 44922200D 00 44922200D 00 4 orbital energy 45973017D 00 10403593D 00 53816730D 00 57914834D 00 40089482D 14 48573263D 00 29510298D 00 29510298D 00 5 orbital energy 39261707D 00 26538042D 15 27636653D 14 26424743D
318. in the gen section of the input file The program hfig constructs a starting wave function initial guess for a Hartree Fock calcu lation The output from the program hf ig for a default calculation begins with the line initial wave function generated automatically from atomic wave functions Next a table lists the number of orbitals and of occupied orbitals in each shell having each irreducible representa tion for the appropriate point group Finally the orbital occupation for each shell is listed an occupation of 1 000 indicates a closed shell An example for a calculation of water using a 6 31G basis set follows start of program hfig initial wave function generated automatically from atomic wave functions Irreducible Total no No of occupied orbitals representation orbitals Shell 1 Shell_2 Al 12 3 A2 2 0 B1 4 1 B2 7 1 Orbital occupation shell 1 000 end of program hfig If the molecule contains a transition metal atom there may be several ways of occupying the d orbitals In this case hfig prints a list of the possible states and continues with the first of these It is possible however that a different initial occupation of the metal d orbitals would lead to a lower energy wave function To see whether this is the case you should run an SCF calculation for each of the possible degenerate states by selecting the state with the istate keyword An example for the FeH molecule follows Low energy states b
319. ine name The host setting is only needed if the name line does not give the machine address You might for example want to provide an alias in the name setting and define the host name in a host setting if the host name is long Another possible use of multiple entries for a single machine is to specify different settings on a machine such as different scratch directories or different software installations You can also use the name and host settings to specify a batch queue name and the host on which the batch system is available The host name does not need to include the full Internet address unless the host on which you plan to run the execution host is not on the same local network as the host from which you plan to submit jobs the submission host The value 1ocalhost is a special name setting that means the host from which the job was submitted In addition to this function the localhost entry sets the default values of settings for all other entries In the schrodinger hosts file example above the host entries ahost and bhost inherit the schrodinger setting from the localhost entry 11 1 2 The user Setting If you have different user IDs on the submission and execution hosts you must include a user setting for the execution host in the schrodinger hosts file on the submission host This schrodinger hosts file must be a local copy 11 1 3 The tmpdir Setting The tmpdir setting specifies a directory where directories for temporary
320. ing Pulay s Modified Scaled Quantum Mechanical Force Fields SQM method 1 Scale frequencies using Pulay s SQM method and use scaled frequen cies for thermochemical calculations only allowed for B3LYP calcu lations with the 6 31G basis set scalfr gt 0 Scale vibrational frequencies by this factor default is 1 0 and use scaled frequencies for thermochemical calculations Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File 200 Table 9 26 Keywords for frequency related properties Continued Keyword Value Description irder 0 Do not compute dipole derivatives or IR intensities for vibrational fre quencies 1 Compute derivatives of dipole moment and IR intensities for vibra tional frequencies see text for details press gt 0 Pressure for thermochemical calculations from frequencies in atm default is 1 0 tmpini gt 0 Initial temperature for thermochemical calculations in K default is 298 15 tmpstp gt 0 Temperature step size difference between consecutive temperatures for thermochemical calculations in K default is 10 0 ntemp gt 0 Number of temperatures at which thermochemical properties are com puted default is 1 When the calculation of vibrational frequencies is requested with ifreq 1 for closed shell Hartree Fock calculations intensities for the IR active vibrational modes are automatically calculated irder is set to 1 automatically For any other level of theory you mu
321. ing the coefficients for He centered short range basis functions the home atom line of the set has a value of 1 entered in the eleventh column meaning that an s type contracted function will be calculated using the exponents provided for the first contracted function for He in the basis set Since this basis set only provides one contracted function for He the 1s function whose derivative is a p type function the last number entered on that line 2 dictates that a p type function be constructed using the contraction coefficients and exponents that correspond to that derivative function as explained in the previous paragraph 10 3 2 Sample File The following sample daf file lists the dealiasing set for H and He for a 6 31G basis set Blank lines may be added for readability and data may be spread over multiple lines dafv0300 5 6 number of sets atom number of rows set 3 0 5 0 7 0 9 0 neighbors cutoffs distances neighbors row 2 Jaguar 6 0 User Manual Other Jaguar Files Chapter 10 BASIS 6 31G H 1102 0 040634 0 080953 0 161278 0 321306 0 640122 1 275283 2 540684 5 061679 10 084136 1 100000 He 2102 0 071497 0 145957 0 297964 0 608279 1 241774 2 535023 5 175131 10 564786 21 567514 1 100000 253 Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files 254 ooo oco O OO OC Ou CO oO U0 TN YW O O O Wo W OG C NN OU ooruuo ooo oo c c ooo 95005 CO O u NO oorrro c
322. input file or from several different templates The jaguar batch command then generates the input files and runs the corre sponding jobs either consecutively if only one host has been specified or by distributing the jobs over the specified hosts 11 3 1 Batch Input File Format Batch input files can include directives job specifications UNIX commands and comments Lines that contain comments must begin with a symbol and lines that contain Unix commands must begin with a symbol Blank lines can also be used in the batch script and are ignored The available directives are summarized in Table 11 6 The directives apply to all jobs described below them unless a later line of the same type replaces them Any OUTDIR TEMP EXEC or FLAGS directive replaces any earlier setting made by the same directive and any of these settings can be reset to their default values with the value NONE for instance FLAGS NONE An OPTIONS directive clears all previously set options and creates a new options list An OPTIONS directive adds new options to the options list or redefines options already in the options list The syntax for the options set by OPTIONS directives is described later and summarized in Table 11 7 The syntax for job specifications is as follows template name new name options Each job specification defines a single Jaguar job For each job the following steps are taken Jaguar 6 0 User Manual Chapter 11 Running Jo
323. ion If you determine that the SCHRODINGER environment variable has not been defined you must set it If you don t know where the installation directory is ask the person who installed Jaguar Then depending on your shell enter one of the following commands csh tesh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory You should also set the SCHRODINGER environment variable in your shell startup file in the cshrc file in your home directory if you are running C shell for instance by adding the setenv or export command to the file so that it is defined for any shell that is used whether interactively or in a batch job 12 1 2 Including the jaguar Command in Your Path The command jaguar is actually a short script that finds the appropriate version of Jaguar to run and passes on any relevant options to the main Jaguar program If you have set the SCHRODINGER environment variable you can run Jaguar jobs using the command SSCHRODINGER jaguar It is usually more convenient to include the installation directory in your PATH or path environment variable so that you do not need to type SCHRODINGER To determine whether jaguar is in your path enter the command jaguar help If the output from this command is a description of how to use the jaguar command Jaguar is already in your path and you can skip the rest of this subsection Otherwise if the output was an error message like jag
324. ion as described above the initial guess is generated from Jaguar s GVB initial guess routine Otherwise the initial guess provided in the gau file is the final wave function resulting from the Jaguar SCF calculation performed starting from the GVB initial guess 7 6 2 Other Jaguar Options for the gau File You can use a Jaguar input file to run a Jaguar job which generates a gau file See Chapter 9 for a description of input files Selecting the Gaussian input file gau output option described above corresponds to setting the output keyword ip160 to 2 in the gen section of the input file Jaguar 6 0 User Manual Chapter 7 Using Jaguar You can create or edit Jaguar input files by hand making keyword settings corresponding to all of the relevant options described above see Chapter 9 for details If you want you can make some of the desired settings in the GUI use the Jaguar Write dialog box to save a Jaguar input file and edit it by hand later to set other keywords You can generate additional information for the gau file by setting the output keyword ip160 in the gen section of the input file to 3 4 or 5 Setting this keyword to 3 lets you provide an initial guess within the gau file as described for GVB calculations above even if you are doing a non GVB calculation Setting it to 5 allows you to explicitly provide the basis set itself rather than just the basis set name within the gau file This option is useful for speci
325. ion the GVB orbitals within a pair are not orthogonal although they are each orthogonal to all GVB orbitals in other pairs For computa tional purposes it is useful to form orthogonal GVB natural orbitals y and y from the GVB orbitals y and y and their overlap S as follows Wat V pp Spe Poe 5 Vos 7 ar 5 a V pa 7 V pb 5b Vpu P 8 The w orbitals generally have bonding character while the y orbitals are anti bonding The contribution to the GVB wave function from each pair is given by CoeW re 7 CpuY pu py OB Boo 6 where the GVB configuration interaction CI coefficients C and C satisfy the following equations PE Pp 7a Cy 1 8 2 2 Ne c2 C2 21 7b Solving for the optimal GVB orbitals is therefore a matter of determining both the GVB natural orbitals and the GVB CI coefficients that minimize the energy of the GVB wave func tion This energy is given by the equation Jaguar 6 0 User Manual Chapter 8 Theory 2N u 2N 2 2C hu ut gt au uv buv Kyy gvb 8 where u and v range over all GVB natural orbitals bonding and anti bonding and where these orbitals are expanded in terms of the basis functions as shown here N basis Y b3 Ciu The terms A J uw Juv and Kuy are defined by N basis huy Qu M Cine uhr N basis s cac jy Gp N basis uu vv QJ uv bj Eye jv ij N basis N basis 2 Ciyl jy Coy C
326. ion factor term in solvation energy 1 Include first shell correction factor term in solvation energy default for most calculations in water turns on Lewis dot keyword ivanset 1 by default ivanset 0 Do not set van der Waals radii according to Lewis dot structure 1 Set van der Waals radii according to Lewis dot structure lewstr 1st structure by default see Section 9 5 5 on page 176 and Section 10 6 on page 260 kesep 0 Combine terms for all one electron matrices 1 Keep kinetic energy terms nuclear attraction integrals and point charge terms separate Note if isolv 1 or 2 kesep 1 by default isolvg 0 Compute gradients in solvation with method used for Jaguar version 3 5 and earlier 1 Compute gradients in solvation with more robust method for version 4 0 on epsout 80 37 Outer dielectric constant of solvent epsin 1 0 Inner dielectric constant of solvent 144 radprb 1 40 Radius of solvent probe molecule sconv 1 5x10 Solvation energy convergence criterion in Hartrees esolv any num Gas phase energy of molecule in Hartrees used in some restart new ber input files for solvation jobs solvent string Solvent name water benzene chlorobenzene cyclohexane carbon tet carbon tetrachloride dichloroethane 1 2 dichlo roethane methanol nitrobenzene dmso dimethyl sulfoxide Jaguar 6 0 User Manual 195 Chapter 9 The Jaguar Input File 196 9 5 13 Properties Keywords Keywords to request calculation of molecular propertie
327. ion for LMP2 calculations than it does for other wave function types Therefore the first non blank line of the file should begin Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files CALCULATION TYPE 01 with any comment allowed after this string indicating that the information following that line 1s for HF DFT or GVB wave functions After all the information in the file for these calcula tions the file should contain this line CALCULATION TYPE 02 followed by information for LMP2 wave functions 10 6 1 Describing Bonding Types in the Lewis File The bonding type information for HF DFT or GVB wave functions should follow the first line describing the calculation type The first line of this information should begin BONDING TYPE 01 and the rest of the bonding type information should not contain any blank lines except the last line which signals the end of bonding type information Bonding type information should be listed for each relevant element in turn The information for the first atom should follow immediately after the BONDING TYPE 01 label The first char acter of the information for that atom should begin with the atom s atomic number The following lines should describe up to five groups of bonds for that atom Each group must begin with the word Group with no leading spaces and must contain information for bond orders 1 2 and 3 with a comment identifying each bond order The group is a
328. ion model are the dominant terms in our empirical corrections there are also intrinsic errors in the gas phase DFT calculations which are implicitly incorpo rated into the correction scheme The assumption is that these errors are systematic for a given functional group This means that the DFT calculations are required only to reproduce the rela tive energetic changes produced by modification of substituents a less demanding task than absolute pK prediction As the accuracy goal 0 5 pK units is beyond the capabilities of the raw DFT calculations empirical corrections are necessary 14 2 Predicting pK Values in Complex Systems The algorithm described in Section 14 1 on page 310 can be straightforwardly applied in the simplest cases which are characterized as follows 1 There is only one relevant ionizable group in the molecule 2 There is a single relevant conformation of the molecule and this conformation is valid for both the protonated and deprotonated form An example of this situation is acetic acid However it is also possible to use the module in more complex situations In the following sections we explain how this is accomplished 14 2 1 Conformational Flexibility First consider the case in which assumption 1 above holds but the protonated and deproto nated states can each exist in multiple conformations which might be energetically competi tive There are several possible ways in which the conformational proble
329. ion when there are degenerate states in tran sition metal systems Same as setting istate 1 n Perform calculation on state number n n is the index of the state in the output from hfig for degenerate states in transition metal systems If you want to perform an open shell singlet calculation using UDFT or UHF set ioss 1 This option replaces the alpha and beta HOMO with a mixture of the HOMO and LUMO as follows Q HOMO PHomo PLUMO AP 9 HOMO nouo ruwo 2 The orbitals are taken from a closed shell starting guess The LUMO remains the same This option also sets isymm 0 and iuhf 1 Do not use this keyword for transition metals for which you should use the 2spin column in an atomic section to set up an antiferromagnetic guess Note This starting guess does not correspond to the open shell singlet state but is a mixture of singlet closed shell and triplet open shell states The final wave function in a UHF calculation will not necessarily correspond to what would be obtained in an ROHF calculation and might be a mixture of a singlet and a triplet state You should check the value of S in the output to determine the extent of spin contamination In UDFT calculations exchange is handled differently and all that can be concluded is that the final density represents the lowest state This is more correctly described as a spin polarized method rather than an open shell singlet method for UDFT it yields the cor
330. ions which are chosen in order to span the function space represented by the Jaguar 6 0 User Manual 155 Chapter 8 Theory 156 grid more completely than the basis functions alone The operator Q can be calculated for the relevant basis functions using several different sets of grid points where each set of points defines a grid type ranging from coarse to ultrafine In practice not all possible Qig elements are calculated for each basis function i and each grid point g because most basis functions drop off sharply enough that they have no significant value on some or most grid points These functions are classified as short range functions and are grouped together by atom while the remaining functions are classified as long range func tions which are all considered to be in one single group 13 Since Q does not depend on the wave function itself it can be fully computed before the SCF procedure However since the Q for each grid type contains Npasis x Noiq elements where Npasis is the number of basis functions and N the number of grid points which is generally larger than Nasis we sometimes reduce memory demands by only computing and storing the Npasis X Ng matrix S R wR in the program rwr for cases where the Q for that grid type is only needed for one SCF iteration We then assemble the full Q during the SCF iteration for which it is needed After the program rwr has generated the Q or S R wR matrix the prog
331. ions between the components in terms of these letters A line below the table summarizes the calculation type and energy as well as the number of SCF iterations If the input system s spin multiplicity is not singlet the summary of the SCF output also includes a breakdown of the two electron contribution to the energy into Coulomb and exchange parts For each of these parts the contribution from each Hamiltonian is listed The highest occupied molecular orbital HOMO and lowest unoccupied molecular orbital LUMO energies are listed next Finally the energies for each occupied orbital and for the ten lowest energy virtual orbitals are provided with each orbital identified by a symmetry label Virtual orbitals and eigenvalues are determined in the same manner as in ref 113 The virtual orbitals are obtained by diagonalizing H gt f 2J K where f is the occupation of each orbital 1 for a closed shell For closed shell Hartree Fock calculations this definition yields the standard orbitals and eigenvalues Finally the CPU time for the job the machine upon which the job ran and its time of comple tion are noted at the end of the output file 6 3 Output File Content for Various Calculation Types Any time you make a non default setting for a calculation the output from the program pre notes the non default options chosen This output appears above the molecular geometry output from the pre program This section describes the changes i
332. is pure VWN If you want to evaluate the energy of the final post SCF wave function using a particular func tional or combination of functionals you should use the keyword jdft This keyword can take on the same values as idft and the meanings for each value are the same as those described above for idft If jdft 1 you can set up a customized functional using the keywords yhf yexl1 yexl9 yexnln ycorln and ycornln which correspond to the keywords in Table 9 15 e g xexl1 If you do a post SCF DFT energy evaluation you should not perform a geometry optimization or calculate the solvation energy polarizability or any other properties For DFT jobs the keyword vshift is set to 0 2 for hybrid methods or 0 3 for non hybrid methods by default and the keyword idenavg is set to 1 by default to aid convergence More complete descriptions and references for each DFT functional and hybrid are given in Section 4 3 on page 59 Table 9 15 Functional coefficient keywords Keyword Corresponding Functional or Exact Exchange xhf exact exchange Hartree Fock xexl1 Slater local exchange functional xexl8 B97 1 local exchange functional xexl9 Xa local exchange functional xexnll Becke 1988 nonlocal gradient correction to exchange xexnl3 Becke 1998 B98 local and nonlocal exchange functional xexnl4 Perdew Wang GGA II 1991 nonlocal exchange functional xexnl6 Schmider and Becke 1998 SB98 local and nonlocal exchange functional xex
333. ital information followed by the Hartree Fock energy and the LMP2 energy correction which gives the improvement to the energy over the HF value The total LMP2 energy the HF Jaguar 6 0 User Manual 115 Chapter 6 Output 116 energy plus the correction is given immediately afterwards If your job is a local MP2 calcu lation and you want to see the energy from each LMP2 pair use the gen section keyword setting ip170 2 as described in Section 9 5 20 on page 212 6 3 3 GVB If a GVB calculation is performed from a Hartree Fock initial guess the pre program output lists a table of GVB pair information below the list of non default options Since the use of symmetry is turned off automatically for GVB calculations the output from the programs pre and hfig is somewhat different than for a Hartree Fock calculation Also the program gvbig runs after hfig if the GVB initial guess is being generated from the HF initial guess The output from the scf program is more extensive than for a default HF calculation First the number of GVB pairs and the number of GVB orbitals are added to the list of electron and orbital information preceding the table of SCF iteration information Secondly the summary of the SCF output is followed by a breakdown of the two electron contribution to the energy into Coulomb and exchange parts For each of these parts the contribution from each GVB Hamil tonian is listed After this information the intra pair
334. items the atom label for atom 3 the identifier of one of the previous atoms the distance between this atom and atom 3 the identifier of the other previous atom and the angle defined by the three atoms In this example N1 C2 N1 1 4589 C3 C2 1 5203 Ni 115 32 the final line states that atoms C3 and C2 are separated by 1 5203 A and that the C3 C2 NI bond angle is 115 32 The bond angle must be between 0 and 180 inclusive The third atom C3 in this case is placed in the xz plane positive x The fourth line contains seven items the atom label for atom 4 an atom identifier the distance between this atom and atom 4 a second atom identifier the angle defined by these three atoms a third atom identifier and a torsional angle In this example N1 C2 N1 1 4589 C3 C2 1 5203 N1 115 32 O4 C3 1 2036 C2 126 28 N1 150 0 the last line states that atoms O4 and C3 are 1 2036 units apart that the O4 C3 C2 bond angle is 126 28 and that the torsional angle defined by O4 C3 C2 NI is 150 0 This information is sufficient to uniquely determine a position for O4 If the first three atoms in the torsional angle definition were collinear or very nearly collinear O4 s position would be poorly defined You should avoid defining torsional angles relative to three collinear or nearly collinear angles In such a case you should use dummy atoms to define the torsional angle see Section 3 4 5 on page 39 The torsional angle is the angle betwe
335. its This keyword can be used to reduce mixing of the real and virtual orbitals which sometimes helps convergence By default vshift is zero except for DFT calcu lations when the default is 0 2 for hybrid methods or 0 3 for non hybrid methods Non default values should probably be on the order of 0 1 0 5 One of the most important keywords in controlling the SCF is iacscf This keyword should be employed when the SCF fails to converge under the default conditions especially for transition metal containing systems or clusters Start with iacscf 1 and if that does not work then try iacscf 4 iacscf 2 was developed especially for hemes and related molecules while iacscf 3 was effective for graphitic systems Energies obtained with iacsef 2 can be directly compared to energies obtained without using iacscf Energies obtained using other values of iacscf are not comparable because they use different grids or cutoffs Table 9 28 Keywords for methods used in the SCF convergence procedures Keyword Value Description iuhf 0 Restricted open shell ROHF or RODFT calculation 1 Unrestricted UHF or UDFT calculation iconv 0 Convergence via Fock matrix diagonalization 1 DIIS convergence scheme default choice for most non GVB calculations see iconv 4 3 OCBSE convergence scheme 4 GVB DIIS convergence scheme default for GVB open shell singlet cal culations and calculations whose initial guess is obtained from Hj maxit
336. ity matrix elements which is controlled by the keyword dconv the usual SCF energy convergence criterion econv is ignored for optimizations If you want to save the structure at each step of a geometry optimization in a Maestro formatted file set ip472 2 You can also extract the structures from the output file to a Maestro file with the command jaguar babel ijagout jobname out omacmod filename mae If you import the structures into Maestro you should set the color scheme manually it is not set correctly on import Table 9 21 Geometry convergence criteria keywords Keyword Default value Convergence Criterion For gconvl 4 5x104 Maximum element of gradient gconv2 3 0x10 rms of gradient elements gconv3 1 0x107 Maximum Newton Raphson step not currently used gconv4 1 0x107 rms Newton Raphson step not currently used gconv5 1 8x10 Maximum element of nuclear displacement gconv6 1 2x107 rms of nuclear displacement elements gconv7 5 0x10 Difference between final energies from previous and current geometry optimization iterations Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File 192 9 5 10 Geometry Scan Keywords Keywords for defining the initial wave function and the initial Hessian for geometry scans coordinate scans are listed in Table 9 22 These keywords can also be used with IRC scans Table 9 22 Keywords for geometry scans Keyword Value Description scanhess 0 Use th
337. ity table The connectivity table provided by this option describes roughly how closely the atoms interact Connectivity partially determines whether molecular fragments exist the content of the initial Hessian and many other properties of a calculation The assignment of dealiasing functions for the pseudospectral method also depends upon the connectivities shown in this table which reflect the neighbor ranges defined in the da file See Section 10 3 on page 249 for more information All of the diagonal entries are 0 indicating that the row atom and the column atom for the matrix element are the same atom An entry of 1 indicates that the row atom and the column atom are considered to be bonded because they are separated by a distance less than the sum of their covalent radii times the variable covfac which is 1 2 by default and is also described in Section 9 5 1 on page 174 If a connectivity table entry is 2 the corresponding row and column atoms are each bonded to some same third atom by the defini tion of bonding described above An entry of 3 4 or more means that the atoms are within the third fourth or higher neighbor range of each other Geometry optimization details If this option is selected additional information about the progress of a geometry optimization is printed This output often helps reveal the cause of any problems with optimizations Keyword ip26 2 in the gen section Keyword ip25 2 in the gen section Ke
338. ixing an entry affects only its inclusion you can still rotate translate or modify the structure 2 4 5 Mouse Functions in the Project Table The Project Table supports the standard use of shift click and control click to select objects This behavior applies to the selection of entries and the inclusion of entries in the Workspace You can also drag to resize rows and columns and to move rows You can drag a set of non contiguous entries to reposition them in the Project Table When you release the mouse button the entries are placed after the first unselected entry that precedes the entry on which the cursor is resting For example if you select entries 2 4 and 6 and release the mouse button on entry 3 these three entries are placed after entry 1 because entry 1 is the first unselected entry that precedes entry 3 To move entries to the top of the table drag them above the top of the table to move entries to the end of the table drag them below the end of the table A summary of mouse functions in the Project Table is provided in Table 2 3 Table 2 3 Mouse operations in the Project Table Task Mouse Operation Change a Boolean property value Click repeatedly in a cell to cycle through the possible val ues On Off Clear Display the Entry menu for an entry Right click anywhere in the entry If the entry is not selected it becomes the selected entry If the entry is selected the action is applied to all selected entries
339. job record for each job after it finishes Exit from the batch script 1 The template file template name in is read This file is read from the current working directory 2 Any options that are defined are applied to the contents of the template file Options that are given on the job specification line override options that are specified with an OPTIONS directive Option syntax is given below 3 A new input file new name in is created The new file is written to the directory specified by a WORKDIR directive or if no WORKDIR directive has been given to the current working directory If new name is not specified new name is set to template name If the file new name in already exists it is overwrit ten unless you use the r option described later in this section Jaguar 6 0 User Manual 283 Chapter 11 Running Jobs 284 4 The Jaguar job is run using jaguar run with this new file as input The command line options for the Jaguar job are specified by the FLAGS directive Tem porary files generated during the job are written to the subdirectory new name in the scratch directory and output files are written to the directory listed on the OUTDIR line if given or from the current working directory The template job name can either be the stem of an existing input file or the string JOB If the string JOB is used the batch script is run multiple times substituting for JOB the job names that are provide
340. king change can be removed if its magnitude is smaller than the tolerance you have set which establishes what changes are acceptable In this case you should inspect the symmetrized coordinates in the Edit Job dialog box to insure that symmetrizing had the desired effect and did not discard any important information about the molecular geometry 3 8 Writing Files When you are satisfied with the molecular geometry and the settings that you have made you can either run the job or save the geometry and settings for later use Running jobs is described in the next section To save your input click the Write button at the foot of the Jaguar panel The Jaguar Write dialog box is displayed This dialog box is a file selector with the usual file browsing tools a Filter text box a Directories list a Files list and a Selection text box By default information is displayed in the lists and the filter for the current working directory If you want to write a Jaguar input file containing the geometry and the settings choose Jaguar input from the File Format option menu When you click OK a Jaguar input file is created that is suitable for running a calculation whether from Maestro or from the command line 5 Keyword isymm 0 in the gen section Jaguar 6 0 User Manual 45 Chapter 3 Running Jaguar From Maestro 46 Jaguar Write E x Filter zonel dyall jaguar ini Directories Files dyal1 jaguar A benzene 01 in d
341. kspace Open Close Build panel Open the Build panel or close it if it is open Local transformation Choose an object type for transforming Click to select atoms to transform Open the Advanced Transformations panel Fit to screen Scale the displayed structure to fit into the Workspace and reset the center of rotation Set fog display state Choose a fog state Automatic means fog is on when there are more than 40 atoms in the Workspace otherwise it is off Jaguar 6 0 User Manual NA amp a lee ii Bs Fa Q9 97 Undo Redo Undo or redo the last action Performs the same function as the Undo item on the Edit menu and changes to an arrow pointing in the opposite direction when an Undo has been performed indicating that its next action is Redo Import structures Open the Import panel Save as Open the Save Project As dialog box to save the project with a new name Delete Choose an object type for deletion Delete hydrogens and waters Open the Atom Selection dialog box Delete other items associated with the structures in the Workspace Click to select atoms to delete Double click to delete all atoms Add hydrogens Choose an object type for applying a hydrogen treatment Open the Atom Selection dialog box Click to select atoms to treat Double click to apply to all atoms Adjust distances angles or dihedrals Choose a paramet
342. l 0 025 Mulliken population for basis functions atom func type population Oo 1 S 1 9954 Oo 2 S 0 8942 O 3 X 0 8034 Oo 4 Y 0 9514 Oo 5 Z 1 1426 Oo 6 S 0 8865 Oo 7 X 0 4669 Oo 8 Y 0 6649 O 9 Z 0 8332 Oo 10 XX 0 0085 Oo 11 YY 0 0024 Oo 12 ZZ 0 0052 Oo 13 XY 0 0142 Oo 14 XZ 0 0000 Oo 15 YZ 0 0021 H1 16 S 0 4950 H1 17 S 0 1263 H1 18 X 0 0185 H1 19 Xx 0 0138 H1 20 Z 0 0111 H2 21 S 0 4950 H2 22 S 0 1263 H2 23 X 0 0185 H2 24 X 0 0138 H2 25 Z 0 0111 Atomic charges from Mulliken population analysis Atom O H1 H2 Charge 0 67059 0 33530 0 33530 sum of atomic charges 0 000000 Jaguar 6 0 User Manual Chapter 6 Output You may find it helpful to select the Gaussian function list basis set setting in the Output folder if you want to have more information about the basis functions More information on this output option is given in Section 6 4 on page 135 If both Mulliken populations and multipole moments are calculated the multipole moments are calculated from the atomic Mulliken populations as well as directly from the wave func tion as noted in Section 4 10 2 on page 76 The output lists the multipole moments from the wave function as described earlier the Mulliken populations as described just above and finally the recalculated moments resulting from the Mulliken charges in the same format used for the earlier moment output 6 3 7 5 NBO Calculations Output for NBO calculations appears under the headin
343. larizabilities and hyperpolarizabilities with the coupled perturbed HF method the tensor elements in au appear in the output from the program cpolar which runs after the SCF calculation Alternatively if you use the finite field method to calculate the polar izability and or first hyperpolarizability of the molecule the output includes data from all the SCF calculations involved See Section 4 10 on page 74 for details on the methods used to calculate polarizability and hyperpolarizability The data from the program sc includes the virial ration V T Before each SCF calculation used for the polarizability evaluation the program polar runs and outputs the electric field in au used for the SCF calculation whose output appears immediately afterwards When all calculations needed for the finite difference method have been performed the program polar outputs the polarizability tensor in au the first hyperpolarizability tensor in au if it has been calculated and the dipoles from each SCF calculation along with information about the electric fields used for the dipole calculations An example of output from a polarizability and hyperpolarizability calculation follows polarizability in AU alpha x x 5 551 alpha x y alpha y x 0 000 alpha y y alpha z x 0 000 alpha z v I 0 000 alpha x z 0 000 5 245 alpha y z 0 000 0 000 alpha z z 11 890 I I alpha 7 562 Dalpha 6 497 first hyperpolarizability in AU beta x x
344. late along the X axis Right SHIFT drag horizontally Translate along the Y axis Right CTRL drag horizontally Translate along the Z axis Middle amp Right drag horizontally Zoom Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro 2 3 4 Shortcut Key Combinations Some frequently used operations have been assigned shortcut key combinations The shortcuts available in the main window are described in Table 2 2 Table 2 2 Shortcut keys in the Maestro main window Keys Action Equivalent Menu Choices CTRL B Open Build panel Edit gt Build CTRL C Create entry Project gt Create Entry From Workspace CTRL E Open Command Script Editor panel Edit gt Command Script Editor CTRL F Open Find Atoms panel Edit gt Find CTRL H Open Help panel Help gt Help CTRL I Open Import panel Project gt Import Structures CTRL M Open Measurements panel Tools gt Measurements CTRL N Create new project Project gt New CTRL O Open project Project gt Open CTRL P Print Maestro gt Print CTRL Q Quit Maestro gt Quit CTRL S Open Sets panel Tools gt Sets CTRL T Open Project Table panel Project gt Show Table CTRL W Close project Project gt Close CTRL Z Undo Redo last command Edit gt Undo Redo 2 4 Maestro Projects All the work you do in Maestro is done within a project A project consists of a set of entries each of which contains one or more chemical structures and their associated data In any Maestro session there can be only o
345. late key integral terms for each SCF iteration since storage costs for these terms are prohibitive Most of the fundamental integrals calculated in the pseudospectral method 1 9 are computed in physical space on a grid rather than in the spectral space defined by the basis functions The pseudospectral method takes the density matrix from the wave function at the beginning of each SCF iteration and the values of the integrals on the grid points and manipulates them to produce the necessary operators on the grid then assembles the Fock matrix by transforming these components back into spectral space where the Fock matrix is used in the usual way to generate the wave function for the next iteration For medium and large molecules the additional overhead of the pseudospectral method in computing the transformation between physical and spectral space is vastly outweighed by the advantages of evaluating the integrals in physical space The matrix needed for the transforma tion from physical to spectral space 7 can be assembled before the SCF iterations by calcu lating the least squares operator Q which is given by the equation Q S RwR R w 1 where S is the analytic overlap matrix between the fitting functions and the basis set R is the matrix of fitting functions evaluated at the grid points and w is a diagonal matrix of grid weights The fitting functions used to construct the matrix R include both basis functions and dealiasing funct
346. lculation lewdot 1 by default if igvball gt 0 Find Lewis dot structure s and exit without performing SCF or other later calculations lewstr Print all Lewis dot structures if lewdot 1 or 1 Use structure number lewstr for output and or setting GVB pairs lewstr 1 by default if igvball gt 0 igvball Do not select any GVB pairs based on Lewis dot structure Select GVB pairs for any atoms according to igvbsel and Lewis dot structure lewstr Select heteroatom GVB pairs only according to igvbsel and Lewis dot structure lewstr heteroatom pairs are all pairs whose atoms are differ ent elements except for C H pairs igvbsel N DA t A WwW N Select only sigma GVB pairs Select only pi and second pi GVB pairs Select only sigma pi and second pi GVB pairs Select only lone GVB pairs Select only lone and sigma GVB pairs Select only lone pi and second pi GVB pairs Select sigma pi second pi and lone GVB pairs default when igvball gt 0 Jaguar 6 0 User Manual 177 Chapter 9 The Jaguar Input File 178 9 5 6 LMP2 Keywords The mp2 keyword allows you to request a local Mgller Plesset perturbation theory LMP2 calculation By default LMP2 is off For more information on the local MP2 method see Section 4 5 on page 63 and Section 8 3 on page 161 LMP2 keywords are given in Table 9 7 LMP2 calculations require a basis set that allows the pseudospectral method to be used See Table 4 1 on
347. lculations from the Jaguar panel in Maestro choose pKa from the Jaguar submenu of the Applications menu The Jaguar panel opens with a modified Molecule folder displayed In this folder you can choose the pK atom in several ways Enter the atom label in the Use this atom text box The atom label is the label used in the input file and corresponds to the atom name in Maestro To display atom names for the Workspace structure choose Atom name from the Label atoms button menu in the main toolbar 2 al Select Pick to the right of the Use this atom text box and pick the desired atom in the Workspace structure You should ensure that there is only one entry in the Workspace when you pick the pK atom Select Use pKa atoms from the Project Table When you select this option the Project Table opens if it is not already open If there is no pKa atom property in the Project Table you can add the property and a value for the entry in the Workspace by selecting Pick to add atoms to Project Table then picking an atom in the Workspace structure To add val ues for other entries include them in the Workspace and pick the appropriate atom in each entry Make sure that this property is defined for each structure whose pK you want to calculate Jaguar 6 0 User Manual 325 Chapter 14 The pK Prediction Module 326 Jaguar jaguar EIEE Use structures from Workspace included entries 1 Molecule SCF Symmetry
348. ld also compute a dipole moment for more accurate results since the charge fitting will then include a coupled perturbed Hartree Fock CPHF term as well You might also want to constrain the charge fitting to reproduce the dipole moment as described below Because the CPHF term is compu tationally expensive it is not included in LMP2 charge fitting by default The fit can be constrained to reproduce the dipole moment and other higher moments if spec ified exactly by choosing the combination of moments from the Constraints option menu For LMP2 wave functions only dipole moments are available Keep in mind that the more constraints you apply to electrostatic potential fitting the less accurately the charge fitting will describe the Coulomb field around the molecule The dipole moment from fitting charges only is generally very close to the quantum mechanical dipole moment as calculated from the wave function Constraining the charge fitting to reproduce the dipole moment is generally not a problem but you might obtain poor results if you constrain the fitting to reproduce higher multipole moments However this option is useful for cases such as molecules with no net charge or dipole moment 66 Keyword icfit 1 in the gen section 67 Keyword icfit 2 in the gen section 68 Keyword incdip in the gen section Jaguar 6 0 User Manual Chapter 4 Options Jaguar jaguar i EIEE Use structures from Workspace included entri
349. le 12 2 Other Problems Some other problems you may encounter are detailed below along with solutions or explana tions You cannot read in a particular file as input Make sure you are choosing a file of the right file type Also make sure the file name and not just its directory is really showing up in the Selection text box before you click OK The molecular structure for the calculation is not what you expected it to be If you read in a Jaguar input file the geometry is obtained from that file unless you edit the geometry after reading the file Any geometry you entered before reading the file is erased Also if you symmetrize the geometry or set symmetry on for the calculation as described in Section 3 7 2 on page 44 Jaguar may make small changes to the molecular geometry If these changes are a problem you should avoid symmetrizing the geometry and possibly turn the symmetry option off as well The calculation is not what you expected it to be If you read in a Jaguar input file some of the settings in the file take precedence over settings previously made in the GUI See Section 3 5 on page 41 for more details Also certain settings affect other settings auto matically for instance if you choose to calculate polarizabilities the energy conver gence criterion can be reset to 1 0 x 10 For a GVB job the program exits early and the output states that you need a different number of lone pairs on a particular atom
350. le For a more detailed description of the information in the log file see the previous sections of this chapter After all the individual programs necessary for that job have finished running a note appears in the log file listing the name and location of the output file When the job is finished this too is noted in the log file Jaguar 6 0 User Manual 143 Chapter 6 Output 144 Jaguar 6 0 User Manual Chapter 7 Using Jaguar This chapter provides some information on how to use Jaguar to obtain the results you want It includes information on setting up an initial guess especially for transition metal systems convergence of SCF and geometry optimizations setting up certain kinds of calculations restarting jobs and using Maestro and Jaguar to set up GAUSSIAN input 7 1 Choosing an Initial Guess The speed of convergence and sometimes simply obtaining convergence depends critically on the initial guess In the development of Jaguar we have attempted to provide default initial guesses of high quality These defaults are described below However there are situations in which the default initial guess for the molecule of interest does not lead to convergence or does not lead to the correct state Some suggestions on how to obtain alternative initial guesses are provided in this section 7 1 1 Overview By default for non GVB calculations on simple closed shell systems with no transition metals Jaguar constructs th
351. le path name daf GRIDFILE file path name grid CUTOFFFILE file path name cutoff LEWISFILE file path name lewis GPTSFILE file path name The last six lines are only rarely used Therefore your Jaguar input files will generally take a form as simple as sections describing molecule amp calculation Jaguar 6 0 User Manual 167 Chapter 9 The Jaguar Input File 168 where only the zmat section which contains the geometry is actually required The basis atomig daf grid cutoff and lewis data files are described in Chapter 10 If you want to use non default choices for any of these files you can specify their paths and names on the appropriate lines of the input file If a file name ends with z for example BASISFILE erwin basis Z Jaguar copies the file and uncompresses it You can specify a file on another host or under another account name on that host by listing the file name in the format host fullpath or user amp host fullpath The GPTSFILE line allows you to use grid points and weights from an input file for any one grid used during the calculation The file should have a line for each grid point and each line should list in order the x y and z Cartesian coordinates in angstroms and the weight for that grid point Grid weights are only used in charge fitting so if you don t want to use them use 0 as a placeholder For information about how to use this grid
352. le to run rsh remote shell and rcp remote copy commands on each other If you get a Permission denied error when trying to start a job the rsh command is not being allowed This problem may occur even if the job submis sion host the submission host and the host where the calculation is to be performed the execution host are the same The best method to test whether this problem is occurring is to issue individual rsh commands at a submission host command line prompt such as rsh execution host who where you substitute the name of the host where you want to perform the calculation for execu tion host If both the local and execution hosts are on the same local network ask your system manager about allowing rsh commands between the two which could be done in several ways depending on your system One way is to list hosts which are allowed to connect using rsh to a given host in its etc hosts equiv file It may be necessary to include the name of the submission host in its own etc hosts equiv file if the calculation is to be done on the submission host See your system manager or your UNIX documentation concerning trusted hosts NIS domains or networking for more information If you get an error which refers to problems writing or changing to a temp directory for the job you should make sure that you have permission to write to the directory specified in the Scratch directory option menu in the Start dialog box and that you ha
353. le to the input ADDEND filename ADDEND guess in substitute a value for a old pattern new pattern bond 1 5 variable Do not use any of the characters torang 170 0 1 lt gt in either pattern 11 3 2 Running jaguar batch You can start Jaguar batch jobs from Maestro or from the command line Maestro automati cally creates a simple batch job when you specify multiple structures as input to any Jaguar task See Section 3 10 on page 49 for more information on using Maestro to run batch jobs Jaguar 6 0 User Manual 285 Chapter 11 Running Jobs 286 The syntax of the jaguar batch command is jaguar batch command options batchfilel bat Ljoblist If the batch script batchfile bat uses JOB in job specifications you must supply the list of jobs to substitute in joblist In the command the suffix bat is optional if it is missing it is added to the stem batchfile The jaguar command options REL VER HOST USER WAIT and PROCS described in Table 11 3 and Table 11 4 can be used in the jaguar batch command For distributed batch jobs you can specify a list of hosts with the HOST option The host names in the list must be separated by spaces and if there is more than one host the list must be enclosed in quotes If a host has more than one processor you can select multiple processors either by repeating the host name or by appending a colon and the number of processors to the host name e g cluster 32 There
354. liasing Function Keywords The grid and dealiasing function keywords allow the user to select from among the various sets of grids and dealiasing functions available in the grid and dealiasing grid and daf input files which are described in Section 10 3 on page 249 and Section 10 4 on page 254 and from the grids generated within Jaguar These keywords are used to specify which grid or dealiasing sets correspond to particular descriptions this correspondence is often indicated by keyword values depending on the order of sets in the grid and dealiasing input files For density functional theory calculations the grid keywords gdftmed gdftfine gdftgrad gdftder2 and gdftcphf select various predefined grids for the SCF gdftmed and gdftfine gradient second derivative and CPHF calculations The grids are indexed with negative numbers The default values for these keywords are 10 11 12 8 and 9 They can be assigned other values for example 13 corresponds to an ultrafine grid and 14 to the largest DFT grid that can be defined in Jaguar which has 125 radial shells and uses an angular offset of 30 434 angular points per shell with no pruning To use such a grid throughout a geometry optimization you would set the following keywords gdftmed 14 gdftfine 14 gdftgrad 14 You can also define your own DFT grids using three keywords which specify the number of radial shells the number of angular points per shell
355. like a file name Each section is delineated by a pair of amp or characters The section name follows imme diately after the first amp or Thus for example the general keyword section may begin with amp gen or Sgen and ends with amp or Within the gen section allowed keywords are followed by numerical arguments giving their values whose meanings are explained in Section 9 5 on page 174 At least one spacing character must precede and follow each keyword or keyword value pair For example Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 1 Sections for Jaguar input files Section Description zmat Contains list of atomic coordinates describing molecular geometry in Cartesian or Z matrix format zvar Sets values for zmat section variables coord Specify particular internal coordinates to be used for optimization connect Specify particular internal coordinates to be used when generating coordinates for opti mization tvec Specify reaction coordinate at transition state for IRC calculations gen Sets general control keywords including those describing the calculation performed the grids dealiasing functions and cutoff parameters used the electrostatic geometry and solvation properties calculated and the parameters used and the output generated gvb Sets GVB pairs Imp2 Sets LMP2 pairs for local local MP2 calculations and delocalization of LMP2 pairs
356. ling Parallel Jaguar Parallel Jaguar is currently available for the SGI Linux and IBM platforms The parallel Jaguar executables are installed by default when you install Jaguar After installation the hosts on which you will run Jaguar may need to be configured for parallel execution Installation and configuration instructions are given in the Schr dinger Product Installation Guide and are repeated below Jaguar 6 0 User Manual 297 Chapter 13 Parallel Jaguar 298 In addition to host configuration the file SSCHRODINGER schrodinger hosts must be edited to add entries for the parallel hosts Each parallel host entry must include a processors line that indicates how many CPUs are available on that host This information is used in the GUI to display the maximum number of processors available for a host and to check that this limit is not exceeded For computer clusters that do not use queuing software an entry must be included for each node and the value of processors for each node should be the total number of processors available in the cluster For computer clusters that do use queuing software host entries must be included for each queue that is to be used and value of processors for each entry should be the total number of processors available in the cluster See Section 11 1 on page 269 for details of the format for the schrodinger hosts file For all platforms you should use local disks for scratch space Performance is
357. list of bonded atoms and bond orders for the element being described for example Group 2 for carbon could describe C C and C O bonds by specifying that for bond order 2 Group 2 contains two elements with atom numbers 6 and 8 The first line under each bond order label must list the number of elements in the group for that bond order 2 for the example if this number is nonzero the next line must list the atomic numbers for those elements 6 and 8 in the example Here is the beginning of a sample lewis file illustrating a list of bonding type information for carbon including some comments to further explain the file format CALCULATION TYPE 01 HF DFT GVB BONDING TYPE 01 INFORMATION 6 CARBON Group 1 C H bonds only Group must be here the rest is a comment Bond order 1 this should be a non blank comment line 1 element 1 the atomic number of H Bond order 2 this should be a non blank comment line Jaguar 6 0 User Manual 261 Chapter 10 Other Jaguar Files 262 0 elements Bond order 3 this should be a non blank comment line 0 elements Group 2 C C and C O bonds Bond order 1 0 elements Bond order 2 2 elements 6 8 Bond order 3 0 elements The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines After all the groups have been specified for a particular atom the file should contain a line containing three asterisks to indica
358. ll command the temporary directory for your job still exists and contains all files generated during the job and no output files are copied back to your output directory To kill one of your Jaguar jobs enter the command jaguar kill jobname This command checks all hosts for the specified job and kills all instances of the job with the name jobname To kill a specific job use the job ID which is unique instead of the job name You cannot kill stranded jobs with jaguar kill because the job control facility does not have the necessary information about those jobs 11 2 5 Converting File Formats Jaguar uses the Babel program 24 to convert between many of the file formats used in computational chemistry Babel can read over 40 kinds of input and output file types and writes both cartesian and Z matrix geometry specifications Babel is used in the GUI to read and write files that are not in Jaguar or Maestro format You can also request Jaguar to write out files during a job run using the babel or babelg keywords see Section 9 5 19 on page 209 for more information To convert file formats from the command line you can use the jaguar babel command The syntax of the command is jaguar babel v iinput format input file h d range ooutput format output file split The i and o arguments are required to set the input and output formats respectively The output format keywords are listed in Table 9 31 on page 210 the input
359. ltiple structures only the first structure in the file is converted to the new format Jaguar 6 0 User Manual 281 Chapter 11 Running Jobs 282 11 3 Running Multiple Jobs jaguar batch If you need to run series of Jaguar jobs frequently you can create batch scripts that define the jobs and run them using the jaguar batch command For instance you might want to study the dissociation of a bond by evaluating the molecule s energy at various appropriate bond lengths scan a potential energy surface or perform a Hartree Fock level geometry optimiza tion and then evaluate the energy of the new structure using LMP2 or DFT techniques To use jaguar batch you need a batch input file whose name should end in bat and at least one input file The input files can provide structures in either Maestro or Jaguar format or can provide templates for running the calculations The batch input file tells jaguar batch how to create a Jaguar input file or modify a template input file for each Jaguar job These modifications can include changes to particular bond lengths and angles of the structure changes in the wave function or job type such as changing an HF geometry optimization input file to a DFT single point energy calculation input file changes in the files or directories used for jobs and virtually all other settings made in input files One batch input file can be used to request several different input files either from one template
360. lving higher level methods or open shells may take a few extra iterations Molecules which include transition metals generally converge more slowly however Make sure your job has really converged and did not simply end because it reached the maximum number of SCF iterations a number set in the SCF folder If a job gives poor SCF convergence you can try either modifying the convergence methods used or improving the initial guess To modify the convergence methods try any or all of the following settings Try setting iacscf to 1 2 3 or 4 see Table 9 28 on page 202 for descriptions of each number s function You might need to increase the setting of maxit to 100 or more when using iacscf values of 1 2 or 4 Select GVB DIIS from the Convergence scheme option menu in the SCF folder Gener ally DIIS is the better choice but the GVB DIIS convergence scheme sometimes leads to convergence when DIIS does not Jaguar 6 0 User Manual Chapter 7 Using Jaguar Setthe SCF level shift in the SCF folder to 0 5 or 1 0 The higher the setting the more the virtual orbitals energies are increased before diagonalization and the more the mixing of the real and virtual orbitals is reduced High SCF level shifts can slow convergence by several iterations but can often help otherwise intractable cases to converge Because jobs with SCF level shifts are slightly more likely to converge to excited states you may also want to restart these j
361. ly all A values for these liquids are assumed to be 0 5 For FCC lattices A is 0 7405 and for BCC lattices A is 0 6802 Rapp A K Casewit C J Colwell K S Goddard W A Skiff W M J Am Chem Soc 1992 114 10024 Chirlian L E Francl M M J Comput Chem 1987 8 894 Woods R J Khalil M Pell W Moffat S H Smith V H Jr J Comput Chem 1990 11 297 Breneman C M Wiberg K B J Comput Chem 1990 11 361 Mayo S L Olafson B D Goddard W A III J Phys Chem 1990 94 8897 Jaguar 6 0 User Manual References 61 62 63 64 65 66 67 68 69 70 7 72 73 74 75 76 77 78 79 80 81 Mulliken R S J Chem Phys 1955 23 1833 Glendening E D Badenhoop J K Reed A E Carpenter J E Bohmann J A Morales C M Weinhold F NBO 5 0 Theoretical Chemistry Institute University of Wisconsin Madison WI 2001 Baker J Jarzecki A A Pulay P J Phys Chem A 1998 102 1412 Scott A P Radom L J Phys Chem 1996 100 16502 Hehre W J Stewart R F Pople J A J Chem Phys 1969 51 2657 Hehre W J Ditchfield R Stewart R F Pople J A J Chem Phys 1970 52 2769 Pietro W J Levi B A Hehre W J Stewart R F Inorg Chem 1980 19 2225 Pietro W J Blurock E S Hout R F Jr Hehre W J DeFrees D J Stewart R F Inorg Chem 1980 20 3650 Collins
362. lytic frequency calculations are much faster than numerical frequency calculations However when frequencies are calculated analytically molecular symmetry is turned off for the job Therefore if you want to compute analytic frequencies for large highly symmetric molecules you should first run any other computationally intensive portions of the job such as geometry optimization then use the restart file as input for an analytic frequency job See Section 7 5 on page 150 for information on generating restart files and restarting jobs If you want to calculate frequencies numerically instead make the keyword setting nmder 2 in the gen section of the input file as described in Section 9 5 on page 174 To compute frequencies and any frequency related properties from the Hessian available at the end of a job either an initial Hessian if it was never updated or the updated Hessian select Use available Hessian 4 11 2 Atomic Masses For frequency calculations the atomic mass used for each element is that of its most abundant isotope by default However you can choose to use an average of the isotopic masses weighted by the abundance of the isotopes by selecting Average isotopic masses from the Atomic masses option menu 81 Keyword ifreq 1 in the gen section 82 Keyword ifreq 1 in the gen section 83 Keyword massav 0 in the gen section 84 Keyword massav 1 in the gen section Jaguar 6 0 User Manual 79 Chapter
363. m Babel 24 and must be in a format recognized by Babel Maestro does not read any information other than the geometry from these files If you want other information such as a Hessian you can cut and paste it into a Jaguar input file 3 6 Setting Charge and Multiplicity Apart from the geometry the main setting that you might want to make in an otherwise default calculation is to set the molecular charge and the spin multiplicity You can set these quantities in the Molecule folder The default molecular charge is determined by the formal charges on the atoms in the Workspace The default spin multiplicity is 1 singlet if the molecule has an even number of electrons and 2 doublet if it has an odd number of electrons You can change the charge by entering a value in the Molecular charge text box and you can change the spin multiplicity by entering a value in the Spin Multiplicity 294 1 text box The spin multiplicity is always displayed in this text box If the molecular charge and spin multiplicity settings you make do not agree with your molecular input for instance if your molecule has an odd number of electrons and you set the spin multiplicity to 1 Maestro warns you of the inconsis tency and you must choose consistent values to submit a job 2 Keyword molchg in the gen section 3 Keyword multip in the gen section Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro The charge and spin multiplicity
364. m can be addressed In the current release only method 1 below has been automated It is still possible to carry out the strategies outlined in method 2 however at present you must run multiple jobs and manu ally assemble the data into a final result 1 Perform calculations on one protonated and one deprotonated conformation which are assumed to dominate the phase space due to being lowest in energy in their class This is a reasonable assumption for many problems Note that the lowest energy conformation can be different for the protonated state and the deprotonated state In many cases there Jaguar 6 0 User Manual 313 Chapter 14 The pK Prediction Module 314 are obvious electrostatic reasons why a conformational change upon protonation or deprotonation would occur The program is set up to accept a different conformation for each species The selection of the appropriate conformation can be nontrivial Our recommendation is to do a solution phase conformational search in MacroModel using the MMFF force field and the GB SA continuum solvent model This is a very fast procedure and gives a reasonable ordering of conformational free energies in solution Alternatively you can either construct the conformation by hand or use a gas phase conformational search Pre liminary results indicate that there are situations where a solution phase conformational search is necessary to obtain accurate results 2 Perform quantum chem
365. m the basis set specified with this label For instance amp guess basgss 6 31g If no basgss setting is given or if basgss is set to non standard the basis set for the guess is that specified by the basis keyword setting in the gen section You should ensure that the initial guess given in the guess section is for the this basis set Otherwise a poor or meaningless guess is obtained and the calculation might not converge Similarly the ordering of the basis functions within the set being used must be the same as that used for the ordering of coeffi cients in the guess section This next line of the section should begin with a set of coefficients describing the contribution of each function in the basis set to the first molecular orbital and continue on with similar Jaguar 6 0 User Manual 235 Chapter 9 The Jaguar Input File 236 coefficient sets for each molecular orbital A single line whose content is unimportant should precede each molecular orbital s set of coefficients If you like you can use this line to label the molecular orbital for your own convenience If you choose to write the occupied orbitals or occupied and virtual orbitals from one run and use them in the guess section for another run you must make sure to choose a proper format From the Orbitals window in the GUI you could select occupied orbitals or all orbitals from the What option menu and all elements as f19 15 in list or all elements as f8 5
366. ments of properties such as transition states dispersion interactions hydrogen bonding and conforma tional energies However the scaling of conventional MP2 algorithms with system size is formally nN where N is the number of basis functions and n the number of occupied orbitals due to the necessity of carrying out a four index transformation from atomic basis functions to molecular orbitals In principle it is possible to reduce this scaling by using integral cutoffs as for Hartree Fock calculations However the reduction is noticeably less effective in MP2 particularly for the large correlation consistent basis sets that are required for accurate correla tion effects on observable quantities Thus MP2 techniques have traditionally been used primarily for small molecules Several years ago Pulay and coworkers 46 47 formulated a version of MP2 in which the occupied orbitals are first localized e g via Boys localization 49 and the virtual space correlating such orbitals are then truncated to a local space built from the atomic basis func tions on the local atomic centers orthogonalized to the occupied space Another critical advan tage of LMP2 as for other localized correlation methods such as GVB is that one can very precisely control which region of the molecule is correlated reducing CPU costs enormously The method has been shown to yield an accuracy for relative energies that is if anything supe rior to conventional MP2
367. metries in bohr as well as Angstroms ip70 2 Extra geometry optimization details ip170 2 Localized orbital locations and LMP2 pair energies for local LMP2 calculations full local LMP2 energy correction is sum of pair ener gies ip173 Fock matrix in Boys localized orbital space ip192 2 Extra optimization related information such as the quadratic energy error 3 Same as setting ip192 2 but includes more detailed information such as the Hessian ip193 2 Numerical Hessian in freq output Jaguar 6 0 User Manual 213 Chapter 9 The Jaguar Input File 214 Table 9 32 Output keywords and their settings Continued Keyword Value Description ip194 2 Diagonal force constants in internal coordinates 3 Same as setting ip194 2 but also includes off diagonal force con stants if they are larger than a factor 0 01 by default times the geo metric mean of the corresponding off diagonal elements the value of the factor can be set using the opt194 keyword 4 All diagonal and off diagonal force constants are printed a When any of the keywords is set equal to 1 the corresponding output is not generated 9 5 24 File Output Keywords The file output keywords are the options that cause files other than the usual log and output files to be created All but one of these keywords are set to 1 by default meaning that the file is not created The file output keyword ip151 controls whether or not a Jaguar restart file is written It is the onl
368. mization method if a coordinate with a negative force constant Hessian eigenvalue exists it is critical for this transition vector to be properly identi fied as efficiently as possible since it leads to the transition state Consequently for transition state searches with the standard optimizer when the initial Hessian chosen is a guess Hessian one not calculated numerically or read from a restart file it can be helpful to refine the Hessian during the calculation before using it to compute any new geometries Hessian refinement is especially likely to improve transition state optimizations that employ eigenvector following described in Section 5 3 3 on page 96 because any eigenvector selected for following should be accurate enough to be a reasonable representation of the final transition vector 26 Keyword ifollow 1 in the gen section 27 Keyword ifollow 0 in the gen section Jaguar 6 0 User Manual 97 Chapter 5 Optimizations and Scans 98 To refine an initial Hessian select Hessian refinement in the Transition State folder then enter the number of low frequency Hessian eigenvectors to be used in the refinement in the Low frequency modes text box By default no eigenvectors are used that is no refinement is performed unless the input specifies particular coordinates for refinement Hessians can be refined using any number of the lowest frequency Hessian eigenvectors Refinements involve SCF and gradie
369. mmand line use the following command jaguar pka PROCS nproc jobname acid and base files If the acid and base conformations are similar you need only specify one input file jobname in which can contain a structure for an acid or a base The structure that you supply in the input file should always be a protonated species for the acid and an unprotonated species for the base The calculations will fail if you give the conjugate acid for a base such as an ammonium ion and the conjugate base for an acid such as a carboxylate ion If the acid and base conformations are different you can specify input files for both the acid and the base If you do you must give two filenames in one of the following forms acidfile deprot basefile basefile prot acidfile prot acidfile deprot basefile deprot basefile prot acidfile The input file name for the acid is acidfile in the input file name for the base is basefile in In this description acid means either the acid or the protonated base and base means the base or the deprotonated acid Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module The structures that are specified in these files must have the same protonation state Thus if you specify an acid in acidfile in the file basefile in must also contain a structure for the acid but in the conformation that is appropriate to the conjugate base Jaguar automatically changes the protonation state and
370. more effectively Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File To control the internal coordinates used in an optimization you should first make sure that Jaguar is going to generate internal coordinates for the job Optimization jobs generate and use redundant internal coordinates unless you have set the keyword intopt in the gen section of your input file See Section 9 5 9 on page 186 for more details To specify that particular bonds or angles should be included in the internal coordinates gener ated and used for an optimization use a coord section Each line of a coord section should contain a list of atoms used to specify a bond bond angle or torsional angle coordinate to be included among the internal coordinates generated by Jaguar If you want to hold a coordinate fixed at its initial value throughout the job add the entry to the end of the line after one or more spaces As an example the coord section amp coord C1 C2 Cl C2 C3 C1 C2 C3 ca amp requests that the set of internal coordinates include the C1 C2 bond the C1 C2 C3 bond angle which is to be held frozen throughout the optimization and the C1 C2 C3 C4 torsion You can specify a value after the sign separated by a space If this value is different from the current value of the coordinate according to the geometry it will be used as a dynamic constraint For example consider the following zmat section for water in which the
371. my Atoms in Z Matrix Input eee eee rere teeta 39 3 4 6 Constraining Z Matrix Bond Lengths or Angles seeeseese 40 3 47 Gountenpolse Galeulations saaie euere Treuen ERITREA 40 3 4 8 Specifying Coordinates for Hessian Refinement ssessssss 40 3 5 Reading Elles ERRARE ARAM dtes age dte D ase tU sess 41 3 6 Setting Charge and Multiplicity sss 42 3 7 Cleaning up Molecular Geometries sss 43 3 7 1 Quick Geometry OptfimizaliOUL 5 a rrr r erri rr pire IEEE ee PREISE EA P REPETI IER 43 3 7 2 SYMMEUIZAUOMN 44 3 8 Writing FIl6S nio egerit tiit n EGER PELLIS AR iode Loss 45 3 9 Running Jobs pios o REED Su a ene ees 46 3 9 1 XOutputiMapnalitig sank RR 47 3 9 2 Job SUBMISSION ODIUOFRS 32 cect sen EEE 48 3 9 3 Starting and Monitoring JOBS ssa oce coa ceret hr tereti eis en 49 Jaguar 6 0 User Manual Contents 3 10 Running Jaguar Batch Jobs sese 49 3 11 OUIDUE 2 are ee na ae ne EIU dI PLI III ME 52 3 12 J2 Theory Calculations 2 rrr pio ep ERAI HE REREEERIRAMA HM eae 52 Chapter 4 Db een 53 43 Molecule Settings i iii mE oH CIR ee 53 4 2 BASIS S6lS Guia pt MER Mmi uiis d ue uut eicere 55 4 3 Density Functional Theory DFT Settings s s 59 4 4 Hartree Fock and CIS Settings sss 63 4 5 Local MP2 Settings using Pd
372. my atom for CH4OH input follows C Oo C 1 421 Hl 1 094 Oo 107 2 X1 C 1 000 Oo 129 9 H1 180 0 H2 C 1 094 X1 54 25 Hl 90 0 H3 C 1 094 X1 54 25 H1 90 0 H4 Oo 0 963 C 108 0 H1 180 0 Jaguar 6 0 User Manual 39 Chapter 3 Running Jaguar From Maestro 40 3 4 6 Constraining Z Matrix Bond Lengths or Angles To freeze bond lengths or angles during a geometry optimization add a sign after the coordi nate values For example to fix the HOH bond angle of water to be 106 0 you could enter the following Z matrix Oo H1 O 0 9428 H1 O 0 9428 H1 106 0 In a geometry optimization on this input geometry the bond angle remains frozen at 106 throughout the optimization although the bond lengths would vary For more details see Section 5 2 on page 90 which describes how to set up constraints for optimizations To constrain two geometric parameters to be the same during a geometry optimization use variables in Z matrix input see Section 3 4 5 on page 39 To freeze variables during an opti mization add a sign to the end of the variable setting in the variable definition section In this example the C H bond is frozen at 1 09 chbond 1 09 HCHang 109 47 3 4 7 Counterpoise Calculations To perform counterpoise calculations you can use a Cartesian or Z matrix geometry that includes counterpoise atoms which have the usual basis functions for that element but include no nuclei or electrons These calculations can
373. n you can determine whether there is a lower or higher symmetry point group that approximately describes the structure and use that group to symmetrize the molecule instead of the default The tolerance is also used when the molecule is symmetrized After translation and rotation the coordinates of the atoms are adjusted to reflect the symmetry group accurately The maximum displacement permitted is the tolerance specified A large tolerance yields the 4 Keyword isymm 8 in the gen section Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Geometry Symmetrizer Tolerance 0 10 Point Group tolerance 0 10 D6h Symmetrize Workspace Close Help Figure 3 4 The Geometry Symmetrizer dialog box highest symmetry but may cause the coordinates to be changed significantly A small tolerance may yield a lower symmetry but results in smaller coordinate changes The main Jaguar programs use a small tolerance 1 0 x 10 bohr which should result in molecular energy changes of 1 microHartree or less You can turn the use of symmetry off in the Molecule folder For methods such as GVB LMP2 GVB LMP2 and for some properties such as IR intensities or hyperpolarizabilities symmetry is not yet implemented and is disabled automatically for the job If you are comparing calculations from geometries that differ only slightly you must use caution when symmetrizing coordinates For example a small symmetry brea
374. n 237 9 14 The orbmiarnm Section oup aia es eA I es 238 9 15 The GCho SECON 25i eiie nette iD et np REESE 239 9 16 The path Section eite thiet retine ttr tpe ee o EXE men 239 9 17 NBO Sections Reale 241 Jaguar 6 0 User Manual Contents Chapter 10 Other Jaguar Files ees 243 10 1 The Basis Set File 0u0000000unsseessnnssnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnennnennnennnn 243 10 1 1 Basis Set Format xiu cen mimis ED Sapa MD une 243 10 1 2 Effective Core Potential Format ccccsccccssssseeeessseeecssseeeeseseeeeesesaeeeees 245 10 1 3 Customizing Basis Sets nein REESE OR XEM a Aida 247 10 2 The Initial Guess Data File sse 248 10 3 The Dealiasing Function File s 249 10 3 1 File Formaband Desetipflolls sim essen 250 103 2 Sampe FE cerdo EA DEFIENDE SIE RPM EFE UE IMS 252 10 4 The Grid Elle ERREUR TRUE REFS ed ee 254 10 4 1 Fil Format and Deseription u u a2 254 10 5 The Cutoff File 208 tiet efecto dte ettet tien 257 10 6 The Lewis File kun aan 260 10 6 1 Describing Bonding Types in the Lewis File eseeeeeeee 261 10 6 2 Describing Hybridization Types in the Lewis File essesss 262 10 6 3 Setting van der Waals Radii From Lewis File Data un 264 10 6 4 Default Behavior for Setting Radii siirsin an 267 Chapter 11 RUNNING JODS nee 269
375. n initial guess for a transition state search 3 7 2 Symmetrization By default Jaguar takes advantage of molecular symmetry whenever possible in order to save CPU time Both Abelian and non Abelian point groups are recognized Generally you should symmetrize the geometry if you plan to use symmetry in the calculation itself Otherwise the input coordinates may not be accurate enough for the desired symmetry to be recognized You can symmetrize the molecule using the Geometry Symmetrizer toolbar button in the Build panel When you click this button the Geometry Symmetrizer dialog box is displayed The point group symmetry is determined as follows After the molecule is translated so that the center of mass is at the origin of the coordinate system and rotated so that the principal axes of inertia are aligned on the coordinate axes symmetry operations reflections rotations and inversions are applied to determine the point group of the molecule When Maestro checks whether a symmetry operation produces an equivalent structure the coordinates of the two structures only have to be the same to within a prescribed tolerance that is each pair of symmetry related atoms is within a distance specified by the tolerance The value of the tolerance can be specified in the Tolerance text box and is 0 04 by default This value ensures that the highest symmetry is found in most cases By changing the value and clicking the Find Point Group butto
376. n is performed in two steps first summing over k to form intermediates A A jig 2 Ci Aug gt 20 k Jaguar 6 0 User Manual 163 Chapter 8 Theory 164 then summing over to yield the integrals in molecular orbital space e 5 Zend 21 Jaguar s local MP2 module also includes analytical corrections similar to those described earlier for Hartree Fock and GVB calculations and a length scales algorithm both of which are explained in reference 13 8 4 Density Functional Theory Density functional theory DFT is based on the Hohenberg Kohn theorem 116 which states that the exact energy of a system can be expressed as a functional depending only on the elec tron density In the Kohn Sham implementation of DFT 117 this density is expressed in terms of Kohn Sham orbitals y occ pa 2 y r 22 similarly to the density expression used for Hartree Fock SCF calculations For simplicity we consider only closed shell systems in this overview of the method The Kohn Sham orbitals are expressed as a linear combination of basis functions x 1r and the coefficients for this expansion are solved iteratively using a self consistent field method as for Hartree Fock However DFT includes exchange and or correlation density functionals within the Fock matrix used for the SCF procedure For DFT calculations the Hartree Fock exchange term K in the Fock matrix is replaced by the exchange correlation potential ma
377. n of B3LYP by Xu and Goddard to include Perdew Wang 1991 gradient correction exchange functional 31 with exchange parametrized to fit Gaussian exchange density 44 Table 9 9 Functional name strings for construction of the dftname keyword Name String idft Value Functional Description S 1 Slater local exchange xa 9 XQ local exchange b 11 Becke 1988 nonlocal exchange Slater local exchange pw 41 Perdew Wang 1991 GGA II nonlocal exchange Slater local exchange vwn 100 Vosko Wilk Nusair local correlation vwn5 200 Vosko Wilk Nusair 5 local correlation pl 300 Perdew Zunger 1981 local correlation ps6 1300 Perdew Zunger 1981 local correlation Perdew 1986 nonlocal gradient correction pw91 4400 Perdew Wang GGA II 1991 local and nonlocal correlation lyp 2000 Lee Yang Parr local and nonlocal correlation If you choose to use the idft keyword you can construct a combined functional from the avail able local and nonlocal exchange and correlation functionals Positive values of idft describe both the exchange and correlation functionals The value of idft can be broken down in the form idft 10000 i 1000 j 100 k 10 I m or idft ijklm where the values of j k I and m determine the exchange and correlation functionals and i specifies particular coefficients for the functionals The functionals themselves are determined as described in Table 9 10 through Table 9 13 Jaguar 6 0 User Manual 181 Chapter 9 The Jaguar Input File
378. n of built in batch scripts Script Description JOBS bat Run a sequence of jobs specified by the input files geopt DFT I bat Preoptimize a geometry at the BLYP 6 31G level then optimize at the BLYP 6 31G level geopt DFT II bat Do geometry preoptimizations at the HF 6 31G and BLYP 6 31G level then optimize at the B3LYP cc pVTZ f level geopt DFT III bat Do geometry preoptimizations at the HF 6 31G BLYP 6 31G and B3LYP 6 31G level then optimize at the B3LYP cc pVTZ f level j2 bat Run a J2 theory calculation 25 pka bat Run a pKa calculation See Chapter 14 for details Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Select Batch Script sj ei x Filter IB builds r2004 2_rc2 jaguar v60009 scripts bat Directories Yjaquar v60009 scripts x1 jaguar v60009 scripts geopt dft I bat geopt dft II bat geopt dft III bat j2 bat pka bat pka deprot bat 1 SI FESEEEEEREREN P Rr _ lz Directory Working Launch Jaguar Scripts Notes Fi iz Selection ne2 0B builds r2004 2 rc2 jaguar v60009 scripts OK Filter Cancel Help Figure 3 9 The Select Batch Script panel The input files that you select can be pre existing input files or files created from the current structure in the Workspace or from Project Table entries These choices are available from the Source of structures option menu in the Run Batch File panel If you choose Workspace or Selected entries th
379. n or smaller unless the fifth integer is 1 in which case the question of the atom s ring environment is ignored completely The size n should not be more than 20 The sixth integer indicates whether the description corresponds to an atom in an aromatic ring as defined by the Huckel Rule 4n 2 electrons in ring where n is a non negative integer If the sixth integer is 1 the description corresponds to an aromatic ring if it is O the description corresponds to a non aromatic ring and if it is 1 the aromaticity of the ring is irrelevant Note however that aromaticity is not evaluated if the fifth integer describing ring size is 1 To describe aromaticity without regard to ring size you should generally set the fifth integer to 20 and the sixth to 1 corresponding to atoms in aromatic rings of size 20 or less 10 6 4 Default Behavior for Setting Radii The radius settings contained in Jaguar s de ault lewis file are used for any relevant atoms in all default solvation calculations in water with Jaguar s solvation module except for calcula tions on ions or on molecules containing atoms with atomic numbers greater than 18 By default the program uses the first Lewis dot structure generated to evaluate the radii and the solvation calculation also includes a correction term the first shell correction factor that depends on that Lewis dot structure If the Lewis dot structure does not correspond to that Jaguar 6 0 User Manual
380. n output for various calcula tion settings described in Chapter 4 Generally only the format changes that result from these settings are discussed below Natu rally these settings will often change the data listed Options that have no significant impact on the output format are not discussed in this section Jaguar 6 0 User Manual Chapter 6 Output 6 3 1 DFT If you use density functional theory for the SCF calculation the output above the SCF table lists the functional or combination of functionals used The energy information for DFT calcu lations includes the breakdown of the two electron energy into Coulomb and exchange corre lation terms For DFT calculations virtual orbitals are obtained by diagonalizing Ho y f 2J V where f is the occupation of each orbital 1 for a closed shell For closed shell calculations this definition yields the standard orbitals and eigenvalues The scf output from post SCF DFT energy evaluations GVB DFT calculations for instance first lists the standard output for the HF GVB or DFT SCF calculation then lists the energy breakdown and total energy from the post SCF DFT analysis Since the post SCF DFT treat ment does not change the wave function no orbital output is reported from this step The output from the program pre for non default options contains the detailed description of customized functional combinations for SCF or post SCF DFT calculations 6 3 2 LMP2 If you perform
381. n phase energy is the total solvent energy which is computed as half of the total of the nuclear solvent and electron solvent terms since some of its effect has already changed the solute energy Third a solute cavity term which computes the solva tion energy of a nonpolar solute of identical size and shape to the actual solute molecule as described in reference 15 is included The last solution phase energy component shown only if it is nonzero is term T the first shell correction factor which depends on the func tional groups in the molecule with atoms near the surface contributing most heavily Finally the list ends with the reorganization energy and the solvation energy The reorganiza tion energy is the difference between the total solute energy and the gas phase energy and does not explicitly contain solvent terms The final solvation energy is calculated as the solution phase energy described above minus the gas phase energy The results of the self consistent reaction field iterations so far performed are summarized after the sc output in the output from the program sole An example from the final SCRF iteration of water in cyclohexane follows start of program sole SCRF solvation energy iteration Hartrees kcal mol 0 0 0000000 0 0000 1 0 0024304 1 5251 2 0 0027473 1 7240 3 0 0027918 1 7519 stopping solvation energy converged iterations 3 sfinal 1 7519 kcal mol end of program sole The solvation energ
382. n to define the second and third geom etries See Section 9 3 for details 9 3 The zvar zvar2 and zvar3 Sections The zvar section should contain a list of equations setting the values of any variables in the geometry input in the zmat section in the same units used for the zmat section Here is a sample zvar section amp zvar ycoor 0 753108 zcoor 0 454006 amp Jaguar 6 0 User Manual 171 Chapter 9 The Jaguar Input File 172 For an optimization to constrain freeze all bond lengths or angles set to a particular variable you should add a sign to the end of the zvar section equation setting that variable Similarly to request Hessian refinement of a coordinate whose value is determined by a variable setting in the zvar section just add an asterisk to the end of the equation that sets the variable value in the zvar section For example the zvar section amp zvar ycoor 0 753108 zcoorz0 454006 amp would freeze all ycoor values to 0 753108 during an optimization job Certain types of transition state optimizations require that you enter two or three geometries see Section 5 3 on page 93 for details For these jobs you can specify variables for the second and or third geometries in the zvar2 and zvar3 sections If no zmat2 or zmat3 sections exist these variables are used in combination with the zmat section to define the second and third geometries The equation that defines a variable can also specif
383. n words used by overlap and kinetic energy integral package excluding final matrices themselves ndisk 1500 Atomic strips of J and K are kept in core rather than on disk if basis functions x Hamiltonians ndisk Hamiltonians 1 for closed shell and 2 for open shell mxpr 100 Pairs of dealiasing functions are organized so that each group s pairs have the same angular momentum values e g a group with pairs with an s and a p function The number of pairs in each group evaluated at the same time by subroutine novoro is restricted so that it is mxpr zmpmem 1 0 For LMP2 single point and gradient code maximum total size allowed for arrays holding partially transformed integrals on grid is 60 MB x zmpmem Table 9 40 Keywords to determine when to compute the full least squares fitting matrix Q Keyword Value Description iqcoarse 0 For coarse grid compute Q on the fly in the program scf 1 For coarse grid compute Q in the program rwr and store on disk for later use iqmedium 0 For medium grid compute Q on the fly in the program scf 1 For medium grid compute Q in the program rwr and store on disk for later use iqfine 0 For fine grid compute Q on the fly in the program scf 1 For fine grid compute Q in the program rwr and store on disk for later use Jaguar 6 0 User Manual 221 Chapter 9 The Jaguar Input File 222 Table 9 40 Keywords to determine when to compute the full least sq
384. nally the first derivatives of the basis set file contracted functions will be calculated and the values listed for these extra functions correspond to the functions generated this way in order of the function they were generated from and within that order of increasing complexity s before p etc For instance if the basis set contained contracted functions for 1s 2s and 2p orbitals the derivatives would be listed in the following order a p type function resulting from the derivative of the 1s func tion a p type function resulting from the derivative of the 2s function an s type function resulting from the first term of the derivative of the 2p function and a d type function resulting from the second term of the derivative of the 2p function The last six lines of the sample daf file correspond to the gradient dealiasing function set for He note that the atomic number specified for those five dealiasing function sets was 2 The first line of this set describes this set s long range dealiasing functions centered on the He atom which will be used when coefficients for long range basis functions are to be calculated as explained above The second value on this line 3 dictates that uncontracted s type and p type 1 2 3 basis functions are to be constructed using the second exponent provided for this atom 0 145957 The second line of the set which describes this set s He centered dealiasing functions to be used when calculat
385. nclude effective core potentials Continued Atoms of Basis Set Included Options Method dfns Refs cc pVTZ H Ar Ca Ga H C F Si Cl pseudospectral 5 89 92 Kr others analytic cc pVTZ f H Ar Ca Ga H C Ne Si Ar pseudospectral 5 89 92 without f Kr others analytic functions cc pVQZ g H F Na Ar H C O pseudospectral others 5 89 without g Ca Ga Kr analytic analytic functions MIDI H Li C F Si H C F P Cl pseudospectral Li 5 93 95 Cl Br I Si Br I analytic TZV H Kr ek Sc Zn X analytic 5 96 p only TZV f H Kr Sc Znp analytic 5 96 and f The other available basis sets which are listed in Table 4 2 include effective core potentials ECPs The names of eight of these basis sets begin with LA to indicate they were devel oped at Los Alamos National Laboratory If the next character in the name is a V the basis set is valence only containing only the highest s and p shells for main group atoms and the highest s p and d shells for transition metals For example 5s and 5p would be included for tellurium and 6s 5d and 6p for tungsten LAV 1 indicates that the basis set has been fully contracted to form a minimal basis set LAV2 that the last Gaussian has been uncontracted to form a double zeta basis and LAV3 that all of the s functions and the last p and d Gaussian have been uncontracted Names starting with LACV indicate that the basis set also includes
386. ndant internal coordinates would include the C1 C2 bond the C2 C3 bond and the C1 C2 C3 angle in addition to whatever internal coordinates would be generated without the connect section 9 5 The gen Section The keywords of the gen section allow control over how the calculation is performed Many of these keywords can be set from the GUI See Chapter 4 and Chapter 6 for details Throughout this section the default values for keywords are indicated in bold italics The keywords for geometry input are described first followed by those relating to correlation methods optimization to a minimum energy structure or transition state calculations in solu tion calculation of various molecular properties basis sets SCF methods and output These subsections correspond to the order of information in Chapter 4 and Chapter 6 Finally keywords relating to grids and dealiasing functions cutoff parameters and memory usage are described 9 5 1 Geometry Input Keywords The keywords iunit and covfac help determine how the geometry input from the zmat section will be interpreted The iunit keyword whose default value is 1 describes what units the geometry is assumed to have as indicated in Table 9 2 The real valued keyword covfac determines which atoms are considered to be bonded Two atoms are bonded if they are closer to each other than covfac times the sum of their covalent radii which are listed in Table 9 45 The default value for this variable
387. ne Maestro project open If you do not specify a project when you start Maestro a scratch project is created You can work in a scratch project without saving it but you must save it in order to use it in future sessions When you save or close a project all the view transformations rotation translation and zoom are saved with it When you close a project a new scratch project is automatically created Jaguar 6 0 User Manual 11 Chapter 2 Introduction to Maestro 12 Likewise if there is no entry displayed in the Workspace Maestro creates a scratch entry Structures that you build in the Workspace constitute a scratch entry until you save the struc tures as project entries The scratch entry is not saved with the project unless you explicitly incorporate it into the project However you can use a scratch entry as input for some calcula tions To incorporate a scratch entry into a project you can do one of the following Click the Create entry from Workspace button E Choose Create Entry from Workspace from the Project menu Press CTRL C In the dialog box enter a name and a title for the entry The entry name is used internally to identify the entry and can be modified by Maestro The title can be set or changed by the user but is not otherwise modified by Maestro Once an entry has been incorporated into the project its structures and their data are repre sented by a row in the Project Table Each row c
388. ned consistently the workaround is to manually add the full path to each of Jaguar s parallelized executables to each user s server apps file on the compute nodes For example if SCHRODINGER is set to opt schrodinger and if you are using v55011 of Jaguar you would need the following entries in server apps opt schrodinger jaguar v55011 bin Linux x86 pjexec psetup opt schrodinger jaguar v55011 bin Linux x86 pjexec cleanup opt schrodinger jaguar v55011 bin Linux x86 allnodeexec opt schrodinger jaguar v55011 bin Linux x86 mpi spread opt schrodinger jaguar v55011 bin Linux x86 ppre opt schrodinger jaguar v55011 bin Linux x86 ponee opt schrodinger jaguar v55011 bin Linux x86 phfig opt schrodinger jaguar v55011 bin Linux x86 pgrid opt schrodinger jaguar v55011 bin Linux x86 prwr opt schrodinger jaguar v55011 bin Linux x86 pscf opt schrodinger jaguar v55011 bin Linux x86 plmp2 opt schrodinger jaguar v55011 bin Linux x86 ppost 13 1 3 IBM Installation For IBM you need to install the Parallel Operating Environment POE package which includes the MPI libraries Jaguar requires a version of POE no earlier than 3 2 Be sure to check the README file in usr lpp ppe poe and the man page for details on POE If you use LoadLeveler it must be a version that is no earlier than 2 1 Jaguar 6 0 User Manual Chapter 13 Parallel Jaguar You may need to set an environment variable in order to use multiple processors for a job
389. nergy structures than it is for transition state optimizations both defaults are in bold italics and the cases for which each is a default are explained in the keyword description Table 9 18 lists keywords specific to transition state optimizations Table 9 19 lists keywords that are used to specify the initial Hessian control Hessian updating and modify the Hessian when using it to update the geometry Table 9 17 General geometry optimization keywords Keyword Value Description igeopt 0 Do not optimize molecular geometry 1 Optimize minimum energy structure 1 Calculate forces but do not perform geometry optimization 2 Optimize transition state geometry nogas 0 For optimizations in solution perform gas phase geometry optimization first to get accurate solvation energy 1 For optimizations in solution skip gas phase geometry optimization and compute solvation energies using esolvO value from input file as gas phase energy should yield same structure as nogas 0 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 17 General geometry optimization keywords Continued Keyword Value Description 2 For optimizations in solution skip gas phase geometry optimization and compute solvation energies using energy of initial structure as gas phase energy should yield same structure as nogas 0 intopt 0 Use Cartesian coordinates for optimization 1 Use internally generated redundant internal coordinates fo
390. netic system the standard transition metal initial guesses do not work For an antiferromagnetic system containing two metal atoms that are not bonded you can use a 2spin column in the atomic section to set up the initial guess When the metals are within bonding distance or when there are more than two metals you should set iopt420 420 in the gen section then manually assign ALL atoms to fragments using the frag column of the atomic section The bonded metals must be assigned to separate fragments All atoms must be assigned because all unassigned atoms are assumed to be in the same fragment Finally add formal and 2spin values in the atomic section Transition metal systems can have multiple states based on different occupations of the d orbitals If this is the case the initial guess routine prints the possible states and by default continues with the first state However this state might not be the lowest state You should run calculations on all the possible states in turn to locate the true ground state You can select states by setting the istate keyword in the gen section to the index of the state listed in the output from hfig An example of this output is given in Section 6 2 on page 110 If you want to examine the coefficients of the MOs to see which state is which set ip105 7 7 2 SCF Convergence Generally Hartree Fock wave functions for simple organic molecules converge in fewer than 10 iterations while complex calculations invo
391. nge function while a 1 2 3 or 4 indicate various types of short range functions These assignments help determine the symmetrization of the Fock matrix components by the side choosing method described in Ref 13 These range values are only used in pseudospectral calculations so if your basis set will be used for non pseudo Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files spectral calculations use 0 as a place holder for each range value Pseudospectral calculations require that grids and dealiasing functions exist for the basis set These are defined in the default grid and default daf files respectively see below The Gaussians in the contraction are listed next with the first number in each of these lines describing the exponent for the Gaussian and the second its coefficient in the contraction The Gaussians should be listed in decreasing size of exponent If both s and p functions are being described the second number on the line corresponds to the coefficient for that Gaussian in the s function s contraction and the third number corresponds to the p function s contraction coef ficient The data for that atom ends with a line containing 4 characters with no spaces or other characters preceding them When all of the atoms for that basis set have been listed ending with the obligatory line the next basis set is listed in the same manner described above The beginning of the default basis file is shown bel
392. nie execution sequence S sample calculation sss 29 31 scaling frequencies sess 80 81 keywords 199 Scan foldet netter rere redet 99 scanning geometries esee 98 102 SCF energy output esses 113 SCF fold niano eet tester rsen 68 accuracy level tne 68 convergence controls sess 70 localization of orbitals 71 SCF iterations keywords entrent es 215 maximum number of 69 148 SCF methods keywords 201 202 SOE PPO STAM ner een 240 GVB calculations eese 117 output from 112 114 116 117 118 120 123 solvation calculations 120 Schrodinger contact information 334 SCHRODINGER directory 289 290 schrodinger hosts file 48 49 269 272 275 294 295 scratch directory eee 283 SCTALCH CHUTES 45 eie rie tete 12 Index Scratch Projects eerte tete tute 11 SCRF method see self consistent reaction field scripts function key macros sess 25 Jaguar batch neeecettie 282 uETU D 25 Maestro command eesesssss 24 Python caeteras dete otim 23 search method transition state 93 second derivative of energy keywords 189 199
393. nl7 HCTH407 local and nonlocal exchange functional Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 15 Functional coefficient keywords Continued Keyword Corresponding Functional or Exact Exchange xexnl9 PBE local and nonlocal exchange functional xcorli VWN local correlation functional xcorl2 VWNS local correlation functional xcorl3 Perdew Zunger 1981 local correlation functional xcorl4 Perdew Wang GGA I 1991 local correlation functional xcornl1 Perdew 1986 non local gradient correction xcornl2 Lee Yang Parr local and nonlocal correlation functional xcornl3 HCTH407 local and nonlocal correlation functional xcornl4 Perdew Wang GGA II 1991 nonlocal correlation functional xcornl6 Becke 1998 B98 local and nonlocal correlation functional xcornl7 Schmider and Becke 1998 SB98 local and nonlocal correlation functional xcornl8 B97 1 local and nonlocal correlation functional xcornl9 PBE local and nonlocal correlation functional 9 5 8 CIS Keywords The configuration interaction singles CIS method can be used after a closed shell Hartree Fock calculation to generate information on excited states The output includes energies oscil lator strengths and transition dipole moments for excitations from the ground state The keywords used to control the CIS calculation are listed in Table 9 16 You should not normally need to set nrestart because the program determines how many iterations it can do with the amount of m
394. ns sese 89 187 refinement of initial Hessian 40 41 97 98 171 172 189 search method sss 93 trust radius esssssss 190 190 191 updating of Hessian esee 189 trial wave function see initial guess troubleshooting ee 289 295 trust radius for optimizations 190 190 194 U undoing Maestro operations esse 26 units TOF PCOMENY ain honte er ti 170 keyWord esinin 175 output options isisisi 137 unrestricted wavefunctions keyword for 6 0 eetedetaoi 202 setting Tor sun nie 59 63 Jaguar 6 0 User Manual user name setting for different hosts 271 utilities JAGEOHVErL Saa e EET EERTE 281 makejbasYtS sceenenitee mer tenerent 247 TOD TEC PL M 301 V van der Waals radii 0220 for ESP fitting iine 76 for solvation calculations 195 input file sections for 226 229 listed in output 120 setting from Lewis file data 264 van der Waals surface sese 75 variables in geometry input 36 37 39 40 91 92 171 172 versions of Jaguar EDT E 215 Ceinume rer 277 Vibration panel 82 vibrational frequencies sess 79 keywords for 189 199 200 Scaling cevesscsuswiverserstensatarasensescess 80 81 199 visualizing in Maestro 82 visualizing with
395. ns with the calculation type and the table of energy results for each iteration skipping the list of information about the molecule s electrons and orbitals The energy information below the table includes several additional terms whose relations to each other are described with the usual alphabetic labels First the total of the terms with no electron contribution is listed term A followed by terms B and C the nuclear nuclear and nuclear solvent energies Next the total one electron energy is listed along with its three components the electron nuclear electron solvent and kinetic energies The total two electron energy and the total of the one and two electron energies the electronic energy follow Term N the total of the Zero one and two electron terms is then listed with the label Total quantum mech energy This term corresponds to the final energy from the sc energy table for that iteration and includes the entire energies for the molecule solvent interactions The output next includes the gas phase and the solution phase energies for the molecule since these terms are of course necessary for solvation energy calculations The first solution phase Jaguar 6 0 User Manual Chapter 6 Output energy component is the total solute energy which includes the nuclear nuclear electron nuclear kinetic and two electron terms but no terms involving the solvent directly The second component of the solutio
396. nsity the output from the program elden appears below the SCF output The output lists the number of grid points used for the electron density calculation and the total number of electrons found over the grid The main output file does not include the charges and grid points for the calculation that information can be found in the output file jobname chdens where jobname in is the input file for the Jaguar job The file jobname chdens lists the Cartesian coordinates and the electron density in au respectively for each grid point Jaguar 6 0 User Manual 127 Chapter 6 Output 128 6 3 7 4 Mulliken Populations If you calculate Mulliken populations by atom the atomic charges and their sum is given under the heading Atomic charges from Mulliken population analysis If you calculate them by basis function the atomic charge output is preceded by a section labeled Mulliken population for basis functions listing the atom label basis function index basis function type S for s X for p etc and calculated population If you calculate them by bond the populations by atom and basis function are given as well An example for water in a 6 31G basis set follows Mulliken Bond Populations first nearest neighbor Atoml Atom2 Pop Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop Hl O 0 314 H2 O 0 314 Mulliken Bond Populations second nearest neighbor Atoml Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop Atomli Atom2 Pop H2 H
397. nt calculations for displacements along these modes which allow more accu rate information about the most important modes to be included in the Hessian You can also specify particular coordinates for Hessian refinement If you put an asterisk after a coordinate value Jaguar computes the gradient of the energy both at the original geom etry and at a geometry for which the asterisk marked coordinate has been changed slightly and uses the results to refine the initial Hessian to be used for the optimization To request refine ment of a coordinate whose value is set using a variable add an asterisk to the end of the vari able setting in the line at the end of the geometry input that defines the variables For instance either of the following two input geometries would use both O H bonds and the H O H angle in a Hessian refinement O1 H2 O1 1 1 H3 O1 I I H2 108 0 or ol H2 ol ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For example for the second water input example shown above only two coordinates will actually be refined the O H bond distance which is the same for both bonds and the H O H angle The same would be true for the first example if molecular symmetry were used 5 4 Geometry Scans Geometry scans are a series of jobs
398. ntal data is advisable as the results are rather sensitive to these quantities However the current model is able to robustly handle substituent and conformational effects once a func tional group is parameterized In our work on neutral solvation we have found that it is necessary to supplement parameter ization of dielectric radii with surface area terms to correct for first shell hydrogen bonding A purely electrostatic model is incapable by itself of properly describing such interactions for all molecules For ions these terms are expected to be even larger and more important as the magnitude of the first shell hydrogen bonding interactions are 3 5 times larger than in neutral species However what we have done in the present model is to incorporate these corrections into our overall empirical fitting scheme described below In this fashion all of the errors asso ciated with the various components of the method are subsumed into a small number of param eters characteristic of the functional group in question 14 1 2 Empirical Corrections The results of the above calculation can be assembled to yield a raw pK value Because of the intrinsic errors involved in each step it is necessary to apply an empirical correction scheme to the raw data to yield good agreement with experiment The validity of this scheme can be assessed only by comparison with experimental data For the most important functional groups we have examined a large and
399. o pass additional parameters to the POE or MPI launch commands you can set the environment variable SCHRODINGER POE FLAGS on IBM platforms or SCHRODINGER_MPI_FLAGS on all other platforms to the arguments that you want to pass in For example for verbose output from mpirun on an SGI set the following environment variable csh tcsh setenv SCHRODINGER_MPI_FLAGS v sh ksh bash export SCHRODINGER_MPI_FLAGS v When a parallel job is run on an IBM host the following POE flags are automatically set euilib ip shared_memory yes wait_mode poll When you are choosing the number of processors to use for a parallel Jaguar job divide the number of basis functions for the job by 100 for HF or DFT jobs or 80 for LMP2 jobs then discard any portion of this number after the decimal place This number is the maximum number of processors advised for an efficient parallel run For instance if your molecule had 486 basis functions the maximum number of processors advised for an HF or DFT calculation is 4 and the maximum number of processors for an LMP2 job is 6 You can tell whether a job is running in parallel by looking at its log file jobname 10g If the job is running in parallel the third line of the log file will contain for example Running on 2 processors If there is no such line the job is running in serial mode If you are using a queueing system for your parallel jobs note that the number of processes created by Jaguar is
400. obs without any SCF level shift Change the Accuracy level setting in the SCF folder to Ultrafine This setting causes the job to use denser pseudospectral grids and tighter cutoffs and generally increases compu tational costs by a factor of two to three If the calculation is a DFT job use finer DFT grids You can adjust this setting from the Grid density option menu in the Theory folder This setting also increases the computa tional cost 7 3 Geometry Optimization If you have built a structure in Maestro or suspect that the structure is not very close to the optimized geometry it can be useful to perform a geometry cleanup To clean up a geometry in Maestro using molecular mechanics with a universal force field UFF available for all elements click the Geometry Cleanup button in the Build panel Er For flexible molecules which might adopt one of several possible conformations you might consider performing a conformational search with MacroModel See the MacroModel User Manual for more information If you are performing a geometry optimization and are not starting from a high quality initial molecular structure you might want to do a quick and dirty calculation to obtain a somewhat better geometry then perform a more accurate calculation by starting with the results you have generated already For example if you wanted to perform an LMP2 geometry optimization you could start by performing a Hartree Fock geom
401. ocal and GGA II nonlocal func tional 31 b3p86 Exchange exact HF Slater local exchange functional 29 Becke 1988 nonlocal gradient correction 32 correlation Vosko Wilk Nusair VWN local functional 30 and Perdew 1986 nonlocal gradient correction 35 bhandh 50 exact HF exchange 50 Slater local exchange functional 29 bhandhlyp Exchange 50 exact HF exchange 50 Slater local exchange functional 29 correlation Lee Yang Parr local and nonlocal functional 33 b97 1 Reparametrization of Becke s 1997 hybrid functional 36 by Hamprecht Cohen Tozer and Handy 39 b98 Becke s 1998 hybrid functional including the Laplacian of the density and kinetic energy density terms as well as gradient terms 37 sb98 Schmider and Becke reparametrization of Becke s 1998 functional 38 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 8 Standard functional names for the dftname keyword Continued Name Description mpwlpw91 mpwlk x3lyp Hybrid functional including modification of Perdew Wang gradient correction exchange functional by Adamo and Barone 42 Exchange 2596 exact HF exchange 75 Slater local functional 29 and Perdew Wang 1991 gradient cor rection functional 31 correlation Perdew Wang 1991 GGA I local and nonlo cal functionals 31 Reoptimization of mPW1PW91 functional parameter for prediction of barrier heights by Lynch Fast Harris and Truhlar 43 Extensio
402. oceeded far enough to have found another IRC point no iremode downhill setting is included 9 5 12 Solvation Keywords Most of the solvation keywords correspond to GUI options described in Section 4 9 on page 71 The allowed values for the solvation keywords are described in Table 9 24 Defaults for some of these keywords are not indicated in bold italics since the keywords default values generally depend on other keywords By default Jaguar calculations are performed in the gas phase so isolv 0 and all other solvation keywords are irrelevant The default values for the real valued parameters are for water The solvent can be specified with the solvent keyword instead of the dielectric constant and probe radius this keyword sets these two quantities For solvated geometry optimizations the trust keyword which is described in Section 9 5 9 on page 186 has a default value of 0 1 instead of its usual default of 0 3 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 24 Keywords for solvation calculations Keyword Value Description isolv 0 Do not perform a solvation calculation 2 Perform a solvation calculation using Jaguar s Poisson Boltzmann solver icavity 0 Do not include solute cavity energy term in solvation calculation 1 Include solute cavity energy term default when the solvent is water 2 Force calculation of cavity energy term isurf 0 Do not include first shell correct
403. of altering single coordinates from the original geometry and calculating energies and gradients for the changed geometry continues until all requested Hessian refinement steps have been performed which the output indicates with a line beginning Hessian optimization completed At that point geopt performs a geometry optimization step from the original geometry and the optimization continues until convergence For transition state optimizations the output for iterations that follow any Hessian refinement includes information identifying the transition vector used for that iteration This output includes the transition vector s eigenvalue and the stretches bends or torsions that are its most important components For any optimization iteration using level shifting after any relevant lines of geopt output described above some information on the computed level shift which may then be adjusted to satisfy step size constraints is included in the output For optimization steps past the first geometry change the change in total energy from the previous geometry to the newly calcu lated geometry in Hartrees is listed next The geopt output then lists the maximum element of the analytic gradient calculated by the earlier programs the root mean square of the gradient elements the step size predicted for the geometry change the trust radius for that iteration and if it is smaller than the step size the factor used to scale the step size so
404. of these types of information appears in a column in the table 6 1 2 Reporting Intermediate Results By default only the final results are reported for each job therefore for instance a table of results from three jobs would have three rows of information However you can also request that information from each geometry SCF or gradient calculation be reported in a different row of the results table For instance the command jaguar results title all iterg echange gmax grms u dmax drms dftg out here produces a table showing the convergence of a BLYP geometry optimization of water Geopt Energy Gradient Gradient Displace Displace iter change max rms max rms 1 3 22E 02 2 65E 02 5 53E 02 4 88E 02 2 2 04E 03 3 85E 03 3 18E 03 2 79E 02 1 70E 02 3 7 04E 05 4 19E 04 3 82E 04 1 45E 03 1 01E 03 4 1 04E 06 3 05E 05 2 52E 05 6 13E 05 5 13E 05 Jaguar 6 0 User Manual 109 Chapter 6 Output 110 The last section of Table 6 1 lists options for specifying when to report intermediate and final results from jobs The a11 option which lets you track the progress of a geometry or transi tion state optimization is likely to be the most useful of the options The allscf option can be used for intermediate results in complex non optimizations such as solvation jobs 6 1 3 Reporting Results for Each Atom By default each line of output from a jaguar results command lists inf
405. oice is Standard because it does not require more than one input geometry but if you can provide product and reactant geometries we recom mend selecting LST If you also have a good guess for the transition state select QST 16 Keyword igeopt 2 in the gen section 17 Keyword igst 0 in the gen section 18 Keyword iqst 1 in the gen section Jaguar 6 0 User Manual 93 Chapter 5 Optimizations and Scans Jaguar jaguar EEx Molecule Theory scF Optimization Transition State Properties Solvation Output Search method wv Standard 4 LST v QST Structures Reactant alcohol Choose Product aldehyde Choose Initial LST guess 0 50 Search along Reactant product path Follow same eigenvector Hessian refinement Job blyp 6 31G Transition State Search Start Read Write Edit Reset Close Help Figure 5 2 The Transition State folder Both the LST option and the QST option set up a QST guided search If you select LST Jaguar generates a transition state guess by interpolating between the reactant and product geome tries By default this linear synchronous transit LST transition state guess is midway between the reactant and product geometries This choice is indicated by the default value of 0 5 for the Initial LST guess setting To pick a transition state guess closer to the reactant geometry change this setting to a number b
406. oint density is determined as a spline fit of the density for each shell where each shell s density is determined as the number of points for that shell divided by the shell volume which is the volume between the spheres whose radii are the average of the current and previous shell radii and the current and following shell radii After the flag for the grid information for each atomic grid is provided The first line of each atomic grid section contains two integers one providing the atomic number for that atom and the other giving the number of shells to be described Currently this second number should be 30 or less The next line contains that number of entries defining the radial shell spacing listing the radius of each shell in bohr Grid points for that shell will be placed at that radius in a pattern determined by the integers given in the third line This last line of integers represents the density of the angular grid for each shell The values are explained below The default grid file for Jaguar version 6 0 begins as follows gridv0220 5 24 BASIS 6 31G coarse grid 1 1 6 0 23021 0 71955 1 74518 2 82595 3 94135 6 40743 137731 27 20699 0 45860 0 97184 1 61794 2 40119 3 26487 5 20964 3c great ro Jaguar 6 0 User Manual 255 Chapter 10 Other Jaguar Files 256 3 0 59584 1 69094 3 39571 5 30494 7 49262 11 30338 16 61803 l3 7 9 T 3 I Blank lines have been added between atomic grids for readability D
407. olarizabilities Shieldings are calculated for all atoms including those with ECPs Shielding constants for atoms whose core is represented by an ECP should be treated with caution because the main contributions come from the core tail of the valence orbitals which is largely absent at ECP centers Chemical shifts derived from these shielding constants might display the correct trends but are likely to have the wrong magnitude Jaguar 6 0 User Manual Chapter 4 Options 4 11 Frequencies and Related Properties By selecting Vibrational frequencies in the Properties folder you can request calculations of frequencies infrared ir intensities and thermochemical properties heat capacity entropy enthalpy and Gibbs free energy The results of frequency calculations can be animated in Maestro 4 11 1 Frequencies Vibrational frequency calculations are available for HF GVB LMP2 and DFT wave functions in gas phase or in solution but are not available for GVB LMP2 calculations Numerical frequencies cannot be computed for unrestricted HF or DFT wave functions For gas phase HF and DFT jobs with basis sets that allow pseudospectral calculations and do not include f functions Jaguar computes analytic frequencies See Section 4 2 on page 55 for more information on basis sets Otherwise Jaguar uses energies obtained at perturbed geome tries to calculate the numerical derivatives of the analytically computed forces Ana
408. ole moments through hexadecapole for HE GVB or DFT wave functions and can compute dipole moments for LMP2 wave functions Moments are computed with respect to the center of mass of the molecule Note that LMP2 dipole moments can be computationally expensive since computing them accurately requires coupled perturbed Hartree Fock calculations By default all moments are calculated You can restrict the order of the moments with the keyword ldips in the gen section If you select one of the higher order moments all moments of lower order are also calculated If atomic charges are computed either by fitting of the elec trostatic potential 58 59 or by Mulliken population analysis 61 the multipole moments are also calculated from these point charges for comparison 71 Keyword wispc in the gen section 72 Keyword mulken 1 in the gen section 73 Keyword mulken 2 in the gen section 74 Keyword mulken 3 in the gen section Jaguar 6 0 User Manual Chapter 4 Options 4 10 4 Natural Bond Orbital NBO Analysis When you select NBO analysis a default Natural Bond Orbital NBO analysis is performed at the end of the Jaguar job The output from the NBO analysis is included in the Jaguar output file Other options for NBO calculations can also be specified in the nbo section or in the core choose and nrtstr sections of the Jaguar input file It is not possible to run NEDA Natural Energy Decomposition Analysis calculations from
409. om The values in the third column mean different things depending on their sign The positive numbers mean that the basis function currently being described is composed of that number of primitive Gauss ians starting with the primitive Gaussian for that row and including the appropriate number of rows immediately below it The negative numbers magnitudes indicate the first shell which contributes to the same contracted Gaussian function In the example below the first row has a jcont value of 6 indicating that the first basis function being described is a contracted Gaussian composed of that primitive Gaussian and the primitives in the next five rows The jcont values of 1 in the next five rows indicate that the primitive Gaussians being described are compo nents in a contracted function whose first primitive Gaussian term is listed in the first row The values in the column marked ishl take on nonzero values when basis functions corre sponding to different values as described in the next column use primitive Gaussians with the same exponents Positive values indicate that the same exponents are used in the shell listed that number of rows down a value of 1 indicates that the exponents are provided from a shell listed earlier The values in the next column indicate the angular momentum a value of 1 Jaguar 6 0 User Manual Chapter 6 Output corresponds to an s function 2 indicates a p function 3 a d function and so on
410. oms in that residue 2 6 2 Picking Tools The picking tools are embedded in each panel in which you need to select atoms to apply an operation The picking tools in a panel can include one or more of the following Pick option menu Allows you to choose an object type Depending on the operation to be performed you can choose Atoms Bonds Residues Chains Molecules or Entries then click on an atom in the Workspace to perform the action on all the atoms in that structural unit The Pick option menu varies from panel to panel because not all object types are appro priate for a given operation For example some panels have only Atoms and Bonds in the Pick option menu All button Performs the action on all atoms in the Workspace Selection button Performs the action on any atoms already selected in the Workspace Previous button Performs the action on the most recent atom selection defined in the Atom Selection dialog box Select button Opens the Atom Selection dialog box ASL text box Allows you to type in an ASL expression for selecting atoms ASL stands for Atom Specification Language and is described in detail in the Maestro Command Reference Manual Clear button Clears the current selection X Show markers option Marks the selected atoms in the Workspace Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro For example to label atoms with the Label Atoms panel 1 Choose Atom Labels from
411. on arranged by functional group MOLECULE pKa calc pK exp Deviation HYDROXAMIC ACIDS formohydroxamic 8 0 8 7 0 7 acetohydroxamic 8 4 8 7 0 3 benzohydroxamic 8 4 8 8 0 4 salicylhydroxamic 8 4 15 0 9 2 aminobenzohydroxamic 9 0 9 0 0 0 2 chlorobenzohydroxamic 8 3 7 8 0 5 2 fluorobenzohydroxamic 8 2 8 0 0 2 2 nitrobenzohydroxamic 8 4 7 0 1 4 3 nitrobenzohydroxamic 8 2 8 4 0 2 4 aminobenzohydroxamic 8 9 9 4 0 5 4 chlorobenzohydroxamic 8 4 8 7 0 3 4 fluorobenzohydroxamic 8 4 8 8 0 4 4 nitrobenzohydroxamic 8 2 8 3 0 1 4 hydroxybenzohydroxamic 8 7 8 9 0 2 IMIDES fluorouracil 8 6 8 0 0 6 methylthiouracil 7 9 8 2 0 3 phenytoin 8 3 8 3 0 0 3 3 methylphenylglutarimide 10 1 9 2 0 9 3 3 dimethylsuccinimide 8 8 9 5 0 7 dimethadione 71 1 6 2 1 5 phthalimide 8 5 9 9 1 4 succinimide 9 0 9 6 0 6 BARBITURIC ACIDS 1 benzoyl 5 5 diethylbarbituric 6 4 6 4 0 0 1 5 5 trimethylbarbituric 8 3 8 3 0 0 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation hexobarbital 8 3 8 4 0 1 1 4 nitrophenyl 5 5 diethylbarbituric 77 7 3 0 4 1 5 dimethyl 5 phenylbarbituric 7 5 7 8 0 3 TETRAZOLES 5 cyclopropyltetrazole 5 1 5 4 0 3 5 methyltetrazole 5 0 5 6 0 6 5 hydroxytetrazole 5 4 5 4 0 0 5 phenoxytetrazole 4 2 4 4 0 2 5 phenyltetrazole 4 9 3 5 1 4 tetrazole 4 7 4 9 0 2 PRIMARY AMINES methylamine 10 3 10
412. on Settings Jaguar can treat solvated molecular systems with a self consistent reaction field method using its own Poisson Boltzmann solver 15 141 You can compute solvation energies and minimum energy solvated structures or solvated transition states The solvation energy from a geometry optimization is computed as the difference between the energy of the optimized gas phase structure and the energy of the solvated structure that was optimized in solution In the SCRF method that Jaguar uses Jaguar first calculates the usual gas phase wave function and from that the electrostatic potential and fits that potential to a set of atomic charges as described in Section 4 10 1 on page 74 These charges are passed to the Poisson Boltzmann solver which then determines the reaction field by numerical solution of the Poisson Boltz mann equations and represents the solvent as a layer of charges at the molecular surface which serves as a dielectric continuum boundary These solvent point charges are returned to Jaguar s SCF program which performs another quantum mechanical wave function calcula 56 Keyword ipopsym 1 in the gen section 57 Keyword locpostv 0 in the gen section 58 Keyword locpostv 1 in the gen section 59 Keyword locpostv 2 in the gen section 60 Keyword isolv 2 in the gen section Jaguar 6 0 User Manual 71 Chapter 4 Options Jaguar jaguar EEE Use structures from Workspace included entries 1
413. on energy calculation When the solvation energy has converged Jaguar runs the program pbf once more to get the solvation related gradient This pbf output does not contain the usual solvent accessible surface area and cavity energy terms The programs derla dsolv rwr and der1b then compute the forces with the force table in the der1b output in the usual manner and the program geopt computes the new molecular structure as usual For each new structure generated during the optimization Jaguar first performs the SCRF calculation then obtains the forces in solution and finally generates a new structure The calculation proceeds until the geometry optimization convergence criteria are reached The convergence criteria for optimizations in solution are three times larger than they are for optimizations in the gas phase For solvated geometry optimizations the solvation energy is computed as the difference between the energy of the optimized gas phase structure and the energy of the solvated struc ture that was optimized in solution 6 3 7 Properties If you make any non default selections from the Properties folder the program ch runs and writes the results to the output file after the SCF iterations if any 6 3 7 1 Multipole Moments and Charge Fitting When multipole moments are calculated the x y and z components of the dipole moment and the total magnitude of the dipole moment u are reported in debye followed by information on any r
414. on from orbital 5 the HOMO to orbital 6 the LUMO The transition dipole moment is the amplitude that is used to evaluate the oscillator strength which is a measure of the transition probability Oscillator strengths near 1 indicate strongly allowed transitions From the above output an electronic transition to the second excited state of water is not a dipole allowed transition due to symmetry while the transition to the first excited state is predicted to be only weakly allowed 6 3 10 Basis Set If you selected Gaussian function list basis set in the Output folder or set ipl 2 in the gen section a list of atoms and the basis set used for each atom is given followed by two tables that provide information about the basis set The functions in a basis set are made up of polynomials of the appropriate degree multiplied by linear combinations of Gaussian primitives of the form Nexp zr where N is a normaliza tion constant and z is the exponent of the primitive Gaussian If the linear combination has only one Gaussian primitive the function is called uncontracted otherwise it is called a contracted Gaussian Each shell is defined by a product of a polynomial and a Gaussian primitive The shell information table is printed first An example for water with a 6 31G basis set is given below The first column indicates which atom the shell is centered on The second column lists the shell numbers which increase consecutively for each at
415. on label should begin with the word orient which is followed by an option in the form ab ab a b or a b where a and b are each either x y or z for example amp zmat orient x y Jaguar places the first atom in the Z matrix at the origin the second along the a axis in the negative direction for a and the third atom in the ab plane in the quadrant deter mined by the positive or negative signs of a and b To perform counterpoise calculations you can specify counterpoise atoms which have the usual basis functions for that element but include no nuclei or electrons by placing an sign after the atom labels For example to place sodium basis functions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in a Cartesian input file Nal 0 0 0 0 1 0 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File You can also input counterpoise atoms for geometries in Z matrix format If you are optimizing a molecular structure to obtain a minimum or a transition state you might want to refine the Hessian used for the job See Section 5 3 on page 93 for information on the methods used for transition state optimizations including Hessian refinement If you add an asterisk to a coordinate value Jaguar computes the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightly and will use the results to refine the initi
416. ons jobname job name longjobname job name with wider output stoich stoichiometry weight molecular weight basis basis set nbasis number of basis functions nelectron number of electrons npair number of electron pairs nsigma number of sigma electron pairs npi number of pi electron pairs natom number of atoms symmetry molecular symmetry nsymm symmetry number charge molecular charge multip spin multiplicity s2 spin lt S 2 gt sz2 spin Sz lt Sz 1 gt method SCF post SCF method Energy related options energy final molecular energy enuc nuclear repulsion energy egas gas phase energy esoln solution phase energy esolv solvation energy esolute solute energy 106 Jaguar 6 0 User Manual Chapter 6 Output Table 6 1 Options for the jaguar results command Continued Option Meaning esolvent solvent energy ereorg solvent reorganization energy homo HOMO energies lumo LUMO energies gap HOMO LUMO energy gap zpe zero point energy entropy entropy S at 298 15 K enthalpy enthalpy H at 298 15 K gibbs Gibbs free energy G at 298 15 K cv heat capacity C at 298 15 K int_energy Utot Htot Gtot pka pkb dipole internal energy U at 298 15 K Total internal energy U at 298 15 K including the SCF energy and zero point energy Total enthalpy H4 at 298 15 K including the SCF energy and zero point energy Total Gibbs free energy G at 298 1
417. ontains the row number an icon indicating whether the entry is displayed in the Workspace the In column the entry title a button to open the Surfaces panel if the entry has surfaces the entry name and any entry properties The row number is not a property of the entry Project Table table Table Select Entry Property ePlayer Ay Ez Rel Ie oe e m o mai 2 selected mol 0007 mol 0008 mol 0024 mo1 0034 mol 0039 ni 1 Close Help Included Excluded Fixed or locked Selected entry entry entry entries Figure 2 3 The Project Table panel Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro You can open the Project Table panel by choosing Show Table from the Project menu by clicking the Open Close Project Table button on the toolbar or by pressing CTRL T Ee The Project Table panel contains a menu bar a toolbar and the table itself You can use entries as input for all of the computational programs Glide Impact Jaguar Liaison LigPrep MacroModel Phase Prime QikProp QSite and Strike You can select entries as input for the ePlayer which displays the selected structures in sequence You can also duplicate combine rename and sort entries create properties import structures as entries and export structures and properties from entries in various formats 2 4 1 The Project Table Toolbar The Project Table toolbar contains two groups of buttons and a status display The
418. oordinates bond lengths or bond angles in terms of a variable these coordinates bond lengths or bond angles are constrained to be the same during a geometry optimization The variable becomes the optimization parameter and the coordinates bond lengths or bond angles are set to the value of the variable at each optimization step The effect of using variables depends upon the format of your input structure If your input structure is in Z matrix format you can set several bond length or angle coordinates to the same variable For input in Cartesian format you can use variables to keep several atoms within the same plane during an optimization by setting their coordinates along one axis to the same variable To use variables to set coordinate values from the Edit Job dialog box first type the variable name zcoor for instance where you would normally type the corresponding numerical value for each relevant coordinate You can put a or sign immediately before any variable and you may use several variables if you want When you have entered the full geometry add one or more lines setting the variables For instance in a geometry optimization using the following Cartesian input Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 the H atoms remain in the same xy plane and the same xz plane the molecular symmetry is preserved Whenever Cartesian input with variables is use
419. op that is the scanner will run through all values of the first scan coordinate before updating the others and so on finally looping last over the last scan coordinate For each geometry in the scan the default initial guess for the wave function and the default initial Hessian are taken from the previous geometry You can change this behavior using the scanguess and scanhess keywords in the gen section of the input file 5 4 3 Restarting Scans Scan jobs do not store a record of their progress If you want to restart a scan job that stopped prematurely you must edit the restart file to ensure that the scan starts at the appropriate point 5 4 4 Scan Results The results of scan jobs started from Maestro are incorporated into the Project Table Each scan point is added as a separate entry to the table with the energy and scan coordinates as properties If you want to submit a particular scan point to Jaguar for refinement you can select the corresponding entry as the source of job input You can also use the plot facility to display plots of the energy as a function of a particular coordinate for example Jaguar 6 0 User Manual 101 Chapter 5 Optimizations and Scans 102 An additional output file with the name jobname steps in is written to the working directory whenever a scan is performed This file contains the geometry specifications for each geometry in the scan along with the calculated energies keywords and fo
420. or several more iterations than single point energy calculations If you select forces only for the Optimize geometry setting the programs derla rwr and derlb will run after scf does The forces felt by each atom in the unoptimized geometry will be output from derlb in a table listing each atom and the components of the force upon it in the x y and z directions The x y and z components of the total force on the molecule are listed in the last line and provide a judge of how accurate the force calculations are in most cases since they should generally be zero An example of this force table for a water molecule optimization follows forces hartrees bohr total atom label x y z 1 Oo 0 000000E 00 0 000000E 00 2 620407E 05 2 Hl 0 000000E 00 6 462331E 05 1 291533E 04 3 H2 0 000000E 00 6 462331E 05 1 291533E 04 total 0 000000E 00 0 000000E 00 2 321025E 04 Jaguar 6 0 User Manual 117 Chapter 6 Output 118 When force calculations or optimizations of a system s minimum energy structure or transition state are performed at the LMP2 level the program derib never runs Instead forces are calculated by the programs 1mp2der lmp2gda and lmp2gdb The last of these programs provides a table of output listing the forces on each atom in the same format as the sample table above For geometry optimizations Jaguar prints bond length and angle information in the output from the program pre If you have constrained bond leng
421. or various solvents Solvent Dielectric Constant Probe Radius 1 2 dichloroethane 10 65 2 51 benzene 2 284 2 60 carbon tetrachloride 2 238 2 67 chlorobenzene 5 708 2 72 cyclohexane 2 023 2 78 dimethyl sulfoxide DMSO 47 24 2 41 methanol 33 62 2 00 nitrobenzene 35 74 2 73 water 80 37 1 40 To use a solvent that is not on this option menu you can define it by choosing Other and changing the entries for Dielectric constant Molecular weight and Density The latter two values are used to calculate the probe radius in angstroms see reference 56 If you compute the solvation energy of a minimum energy or transition state structure opti mized in solution your calculation should compare the energy of the optimized solvated struc ture to the energy of the optimized gas phase structure Therefore by default geometry optimizations in solution are performed only after an optimized gas phase structure is computed However if you want only an optimized structure in solution and do not care about the computed solvation energy you can skip the gas phase geometry optimization by selecting Input structure or Value under Gas phase reference energy These options allow you to use a reference energy other than that of the optimized gas phase structure 61 Keyword epsout in the gen section 62 Keyword radprb in the gen section 63 Keyword nogas 0 in the gen section 64 Keyword nogas 2 in the gen section 65 Keyword nogas 1 in the g
422. orbitals you might also want to fix the orbital populations in each symmetry by selecting Fixed symmetry populations in the SCF folder or setting ipopsym 1 By default populations in each symmetry are allowed to vary so that if the default initial guess is incorrect there is a chance of converging to the correct state Of course you must use symmetry for this strategy to be effective 7 1 2 GVB Initial Guess For GVB calculations the GVB initial guess is automatically constructed from the Hartree Fock initial guess by piecewise localization Another option is to use a converged HF wave function as the basis for the GVB initial guess Because this choice requires two SCF calcula tions one for HF and one for GVB it is considerably more expensive than using the GVB initial guess You might want to try this option if you encounter convergence difficulties The third possibility for the GVB initial guess is to read in a GVB wave function from the input file s guess section and to use that as the initial guess for the calculation Keyword isymm 8 in the gen section Keyword ihfgvb 2 in the gen section or keyword ihfgvb 0 if iguess is not 1 Keyword ihfgvb 1 in the gen section Keywords ihfgvb 0 and iguess 1 in the gen section DUAE Jaguar 6 0 User Manual Chapter 7 Using Jaguar 7 1 3 Initial Guess for Molecules Containing Transition Metals For transition metal containing systems particularly organometallics y
423. ormation that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure The options that let you print tables of coordinates forces or charges for individual atoms are listed in the per atom information options section of Table 6 1 You should not use the atom related options with any of the options that request information pertaining to the entire molecule the energy option for instance 6 2 Output From a Standard HF Calculation The contents of a Jaguar output file vary according to the calculation and output selections made This section describes the output file for a standard default single point closed shell Hartree Fock calculation Section 6 3 on page 114 describes the variations in the output file for the calculation options described in Chapter 4 All output files begin with a line listing the job name the machine upon which the job ran and the time the job was started followed by the general copyright information for the version of Jaguar which was used for the run The rest of this section describes output from each indi vidual Jaguar program run for a default calculation The output from the program pre begins with a description of the calculation to be performed the job name the directory containing the executables used to run the job the directory for temporary files comments from the input file if any and the names and paths of any non defa
424. ot required If you have an antiferromagnetic system this algorithm does not work but you can set keywords to ensure that you have the correct guess See Section 7 1 3 on page 147 for details You can also consider performing a calculation on a related system for which you can more easily obtain convergence for example one that is ionized and then use the results of this system as an initial guess for the system of interest When you restart a calculation with an input file generated during a previous run the wave function from the earlier run is read from the guess section and used as an initial guess The guess section is described in Section 9 10 on page 235 Jaguar can read in an initial guess in one basis set and transform it to the basis set requested for the calculation unless either basis set uses effective core potentials If you suspect that the initial guess is leading to the wrong state you can run a calculation with the initial guess only by choosing Initial Guess Only from the Jaguar submenu of the Applica tions menu or setting igonly 1 You can then examine the orbitals in the output If you also generate orbitals surfaces in the Properties folder see Section 4 12 on page 84 you can examine the orbitals in Maestro to see if they are what you expect If the occupied orbitals are not correct you can swap them by including an orbman section in the input file see Section 9 14 on page 238 for more information When you swap
425. ou are experiencing problems running jobs due to memory related failures as described in Section 12 2 on page 294 Jaguar 6 0 User Manual 219 Chapter 9 The Jaguar Input File Table 9 38 Keywords for specification of length scales for sorting of basis functions grid usage and dealiasing function usage Keyword Value Description Default for Iname 1 Only one length scale used Icoarse 2 Basis functions are sorted into Imedium Ifine lufine lgrad short and long range gname 20 Specifies which parameter set from gcoarse 1 gmedium 2 gfine 3 grid file should be used for grid gufine 4 ggrad 4 glmp2 4 e g 2 for second glmp2grad 2 geldens 4 1 Use spherical charge fitting grid gcharge generated within Jaguar for grid listed by name 2 Use cubic charge fitting grid gener none ated within Jaguar for grid listed by name 3 Use cubic electron density grid gen none erated within Jaguar for grid listed by name 6 Use grid and weights from file spec none ified by GPTSFILE line in input file for grid listed by name dname gt 0 Specifies which dealiasing function dcoarse 1 dmedium 2 dfine 3 from the da file should be used dufine 4 dgrad 5 Memory use keywords are listed in Table 9 39 along with their default values and a descrip tion of their uses If you want to change some memory use but do not have a detailed knowl edge of the code do not change the variable mxpr
426. ou can often obtain superior results by improving the initial guess wave function Jaguar automatically generates high quality initial guesses for transition metal containing compounds if you supply the program with information about the charges and spins of the fragments in the compounds it uses that information when generating the guess Here a fragment is defined as either a collec tion of one or more transition metals that are bonded together or one or more non transition metal atoms bonded together Put another way each fragment is simply a group of atoms that would be bonded together even if all bonds between transition metal atoms and non transition metal atoms were broken Typically the system is broken into ligand fragments and transition metal fragments or adsorbate fragments and cluster fragments For example for ferrocene the iron atom is one fragment and the two cyclopentadienyl ligands are two additional fragments To supply Jaguar with information on charges and spins for its high quality initial guess for a transition metal containing system you need to edit the input file either from the Edit Job dialog box which you open by clicking the Edit button or from a terminal window First add the following lines to the bottom of the input file amp atomic atom formal multip amp The exact number of spaces between words does not matter Fill in information for each fragment under the headings atom formal and multip
427. ould be specified in atomic units on the same line The requested prop erties will then be calculated for the molecule in the presence of this field The scf output will also include nuclear electric field and electron electric field terms The convention used in Jaguar for electric fields is to add a term of E r to the no field Fock matrix where E is the electric field and r is the electron position The contribution due to the interaction between the field and each nucleus of position r and charge q is q E r The efields section can contain more than one line describing several different fields In that case the calculations for each given field will be performed in turn Up to 100 electric fields can be specified 9 13 The ham Section By using the ham section and setting the gen section calculation keyword ihamtyp to 3 you can specify the exact coefficients used to calculate the electronic energy for open shell calcula tions The electronic energy is given by the equation E ihr S adit biKy i ij where the sums are over orbitals 20 The number of electron pairs per orbital in each orbital i is indicated by f which can be listed in the ham section and the one electron Hamiltonian for that orbital is given by h The terms a and b are coefficients which can also be specified in Jaguar 6 0 User Manual 237 Chapter 9 The Jaguar Input File 238 the ham section and the J and K terms are Coulomb and ex
428. ouse ensure that it is configured for three button mouse simulation the middle mouse button is simulated by pressing or holding down both buttons simultaneously 2 2 Starting Maestro Before starting Maestro you must first set the SCHRODINGER environment variable to point to the installation directory To set this variable enter the following command at a shell prompt csh tcsh setenv SCHRODINGER installation directory bash ksh export SCHRODINGER installation directory Jaguar 6 0 User Manual 3 Chapter 2 Introduction to Maestro You might also need to set the DISPLAY environment variable if it is not set automatically when you log in To determine if you need to set this variable enter the command echo DISPLAY If the response is a blank line set the variable by entering the following command csh tesh setenv DISPLAY display machine name 0 0 bash ksh export DISPLAY display machine name 0 0 After you set the SCHRODINGER and DISPLAY environment variables you can start Maestro using the command SCHRODINGER maestro options If you add the SCHRODINGER directory to your path you only need to enter the command maestro Options for this command are given in Section 1 1 ofthe Maestro User Manual The directory from which you started Maestro is Maestro s current working directory and all data files are written to and read from this directory unless otherwise specified see Section 2 8 on page 25
429. out and log in as yourself Second if your X server and the host from which you start Maestro the launch host are not the same machine the X server might not recognize the right of that host to display To correct this problem type the following in a window on your X server xauth nextract displayhost 0 0 rsh ihost xauth nmerge Here ihost should be replaced by the name of the launch host Also the remote shell command should be used for rsh usually bin ucb rsh serves this purpose but rsh gives usr bin remsh on some machines If the restricted shell rsh precedes the remote shell version in your path you must use the full path name If the xauth command listed above results in the message xauth Command not found your path probably does not include usr bin X11 and you should include usr bin X11 in your path You could also substitute usr bin X11 xauth for xauth in the command and try again If the xauth command yields Permission denied the rsh command was not allowed and you should read the paragraphs on rsh and rcp commands in Section 12 1 5 on page 293 Jaguar 6 0 User Manual 291 Chapter 12 Troubleshooting 292 If you have problems running the xauth command described in the above paragraph an alter native is to simply type xhost ihost on your X server This command allows anyone including yourself logged onto ihost to run X programs on displayhost Since this command is a potential security
430. ow to illustrate most of these points BASIS STO 3G STO3G STO 3 STO3 5D H S 0 2 1 1 0 3 42525091400000 0 154328967294599 0 623913729800000 0 535328142281266 0 168855404000000 0 444634542184440 KKKK He S 0 3 2 6 36242139400000 0 154328967291452 1 15892299900000 0 535328142270350 0 313649791500000 0 444634542175373 KKKK Li S 0 3 x 4 16 1195747500000 0 154328967293323 2 93620066300000 0 535328142276839 0 794650487000000 0 444634542180763 SP 0 ds 2 1 0 0 636289746900000 9 996722918659862E 02 0 155916274998087 0 147860053300000 0 399512826086407 0 607683718592546 4 808867839999999E 02 0 700115468876179 0 391957393095192 kkk 10 1 2 Effective Core Potential Format Basis sets containing effective core potentials ECPs are described in a slightly more compli cated fashion First the string ECP must appear between the 5D or 6D label and the BACKUP label This string indicates that the basis set description contains information about the effec tive core potential associated with the basis set Jaguar 6 0 User Manual 245 Chapter 10 Other Jaguar Files 246 As for the basis sets without effective core potentials each atom in the set is described in turn The description begins with the basis function which is in the same format as those described above After a line with two asterisks the effective core potential is described The first line in the effective core potential description contain
431. p Deviation ALCOHOLS methanol 16 7 15 5 1 2 ethanol 16 4 15 9 0 5 2 chloroethanol 15 2 14 3 0 9 2 2 dichloroethanol 14 0 12 9 1 1 2 2 2 trichloroethanol 12 6 12 2 0 4 2 2 2 trifluoroethanol 11 3 12 4 1 1 1 propanol 16 4 16 1 0 3 2 propanol 16 2 17 1 0 9 1 2 propanediol 15 6 14 9 0 7 3 propenol allyl alcohol 15 5 15 5 0 0 3 propynol propargyl alcohol 13 4 13 6 0 2 2 butanol 17 2 17 6 0 4 t butanol 16 7 19 2 2 5 PHENOLS phenol 9 8 10 0 0 2 4 aminophenol 10 6 10 4 0 2 4 chlorophenol 9 4 9 4 0 0 4 fluorophenol 9 6 9 9 0 3 4 methoxyphenol 10 4 10 2 0 2 4 methylphenol 10 3 10 3 0 0 4 nitrophenol 1 2 7 2 0 0 4 hydroxybenzaldehyde 7 8 7 6 0 2 CARBOXYLIC ACIDS formic 3 1 3 0 6 acetic 4 0 4 8 0 8 trifluoroacetic 0 5 0 5 0 0 2 hydroxyacetic glycolic 3 2 3 8 0 6 Jaguar 6 0 User Manual 317 Chapter 14 The pK Prediction Module 318 Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK exp Deviation 2 oxoacetic glyoxylic 1 8 3 0 1 2 propanoic 4 5 4 9 0 4 2 chloropropanoic 3 2 2 9 0 3 3 chloropropanoic 4 3 4 1 0 2 pentafluoropropanoic 0 4 0 4 0 8 2 methylpropanoic 4 8 4 6 0 2 2 2 dimethylpropanoic 4 5 5 0 0 5 3 nitropropanoic 4 1 2 6 1 5 acrylic propenoic 3 6 4 2 0 6 cis 3 chloropropenoic 4 0 3 5 0 5 trans 3 chloropropenoic 3 7 3 8 0 1 propynoic propargylic 2 1 1 9 0 2 3 chloropropynoic 2 6 1 8 0 8 cis 2 methylcyclopropanoic 4 3 5 0
432. page 142 on the log file for more information on this data You can close the Monitor panel by clicking the Close button If you want to reopen it later you can do so by choosing Monitor Jobs from the Applications menu in the main window When the job finishes its output file is copied to the directory from which you started Maestro The output file ends with the extension out For instance if you entered the job name h2o the output file would be h20o out If you want to exit Maestro choose Quit from the Maestro menu in the Maestro main window The Quit dialog box permits you to save a log file of the Maestro session For this exercise choose Quit do not save log file A warning dialog box is displayed which permits you to save the Maestro scratch project For this exercise choose Discard To check that the job ran correctly change to the directory where the output file was stored and enter the following command diff w jobname out SSCHRODINGER jaguar vversion samples H20 out If there is no output from this command the job ran correctly If there is output examine the differences between the two files to see if the differences are significant If you are satisfied with the results of this sample run continue this chapter to learn more about using Maestro If you were unable to run the sample calculation see the troubleshooting suggestions in Chapter 12 Jaguar 6 0 User Manual 31 Chapter 3 Running Jaguar From Maestro
433. pdate Hessian using Powell method 125 3 Update Hessian using mixed Murtagh Sargent Powell method 126 default for transition state optimizations 4 Update Hessian using Murtagh Sargent method 127 not recom mended 1 Compute quantum mechanical Hessian at each geometry sets inhess 4 irfo 0 Before using Hessian to update geometry modify it by sign flipping or reverting to an older Hessian 124 1 Before using Hessian to update geometry modify it by RFO rational function optimization level shifting 129 Default for geometry optimi zations that do not use dynamic constraints 2 Before using Hessian to update geometry modify it by P RFO parti tioned rational function optimization level shifting 129 Default for transition state searches Automatically set for geometry optimizations that use dynamic constraints Jaguar 6 0 User Manual 189 Chapter 9 The Jaguar Input File 190 In order to avoid changing the geometry too much because of an unusually shaped potential well or an inaccuracy in the Hessian Jaguar restricts the norm of the changes to the Cartesian or internal coordinates to be less than a certain trust radius which is defined in atomic units bohrs and or radians The trust radius can vary from one iteration to another itradj 1 or it can be fixed itradj 0 Keywords controlling the use of a trust radius are listed in Table 9 20 If the trust radius is fixed it remains the same throughout the optimi
434. pole moments Calculate dipole and quadrupole moments Calculate dipole quadrupole octupole and hexadecapole moments 1 2 3 4 Calculate dipole quadrupole and octupole moments 5 0 ipolar Do not calculate polarizabilities or hyperpolarizabilities 2 Calculate polarizabilities and first and second hyperpolarizabilities B and y using CPHF method Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 25 Keywords for charge fitting multipole moment and polarizability and hyperpolariz ability calculations Continued Keyword Value Description 1 Calculate polarizabilities and hyperpolarizabilities B using CPHF method 1 Calculate polarizabilities using 3 point finite field method 2 Calculate polarizabilities and hyperpolarizabilities using 3 point finite field method 5 Calculate polarizabilities and hyperpolarizabilities using 5 point finite field method 4 Calculate polarizabilities and hyperpolarizabilities using 7 point finite field method efield 0 024 Electric field for polarizability and hyperpolarizability calculations in au default is 0 006 for ipolar 1 Idens 0 Do not calculate electron density 1 Calculate electron density on grid grid choice set by grid keyword geldens ultrafine grid used by default 1 Calculate electron density on grid and write chdens file in a format that can be converted to a file Anthony Nicholls program Grasp can read using ps2grasp f available
435. ppercase letters can be used The polarization and diffuse function options are described by adding or immediately after the basis name The meaning of these symbols is also described in Section 4 2 on page 55 Neither polarization nor diffuse functions are used if none of these options are specified The tables in Section 4 2 list the basis sets and indicate which options and atoms Jaguar currently accepts for each The other keyword relating to the basis set numd allows you to choose whether to use five or six d functions in each d shell If you do not set numd explicitly the number of d functions is set automatically depending on the basis set as described in Section 4 2 Possible settings for numd are shown in Table 9 27 Table 9 27 Keyword to determine the number of d functions Keyword Value Description numd 5 Use 5 d functions regardless of basis set 6 Use 6 d functions regardless of basis set 9 5 16 Keywords for SCF Methods Many of the keywords that control the SCF calculation can be set from the SCF folder as described in Section 4 8 on page 68 The other keyword settings corresponding to SCF folder settings are described in Section 9 5 18 The SCF keywords are described in Table 9 28 The keyword settings for convergence are somewhat complicated and the defaults vary depending on the settings of other keywords The keywords for convergence thresholds are econv the energy convergence criterion which is t
436. project table that includes a V button in the Vib column with which you can open the Vibration panel You can also generate a Molden input file after a frequency calculation enabling you to visu alize the frequencies with this program See Section 9 5 21 on page 214 for more information on writing a Molden input file 4 11 5 Infrared Intensities Infrared intensities can be computed analytically for closed shell HF wave functions in which the basis set does not have any effective core potentials or numerically for HE GVB or DFT wave functions To calculate infrared intensities for each frequency in km mol select IR Inten sities For closed shell HF calculations of IR intensities molecular symmetry is not used For calculations for which frequencies are computed numerically the numerical derivative of the dipole moment is used for IR intensity calculations Analytic IR intensities are only available with closed shell HF calculations If you want IR intensities for molecules in which the frequencies would normally be calculated analytically the frequencies must be computed numerically by setting nmder 2 in the gen section 4 11 6 Thermochemical Properties Thermochemistry calculations of the constant volume heat capacity C internal energy U entropy S enthalpy H and Gibbs free energy G at standard temperature and pressure are performed by default whenever vibrational frequencies are calculated Rotational symmetry numbe
437. ptions for Orbitals sse 139 6 7 The bog File 2o mono qoa o p FORO D OD SUO I Iu OUS t Eus 142 Chapter 7 Using Jamara 145 7 1 Choosing an Initial Guess s sss 145 ren OVGINIGW ERE TE 145 7 1 2 GVB Initial meee 146 7 1 3 Initial Guess for Molecules Containing Transition Metals 147 7 2 SCF Convergence sse 148 7 3 Geometry Optimization npn Rennen 149 7 4 Setting Up GVB Calculations sssseeeeeeeneennns 150 7 5 Restarting Jobs and Using Previous Results ssssss 150 Jaguar 6 0 User Manual vii Contents viii 7 6 Generating Input Files for GAUSSIAN seneneees 151 7 6 1 Making Input Files for GVB Calculations eene 152 7 6 2 Other Jaguar Options for the gau File eeeeee 152 7 6 8 Writing Orbitals Tor GAUSSIAN opi RAS DRE ARR ALO A Erba MR steeds aiaa E NAR 153 Chapter 8 Theater ia 155 8 1 The Pseudospectral Method sse 155 8 2 Pseudospectral Implementation of the GVB Method 157 8 3 Pseudospectral Local MP2 Techniques see 161 8 4 Density Functional Theory eese nennen 164 Chapter 9 The Jaguar Input File 167 9 1 General Description of the
438. put File Table 9 13 Values of j in idft where idft ijklm jin idft Non local Correlation Functional J 0 none J 1 Perdew 1986 nonlocal gradient correction J Lee Yang Parr local and nonlocal correlation j 3 HCTH407 nonlocal correlation functional j 4 Perdew Wang GGA II 1991 nonlocal correlation only J 6 Becke 1998 B98 nonlocal correlation functional J 7 Schmider and Becke 1998 SB98 nonlocal correlation functional j 8 B97 1 nonlocal correlation functional J 9 PBE nonlocal correlation functional Table 9 14 Values of i in idft where idft ijklm i in idft Hybrid Method i 0 none i 1 half amp half functional coefficients are all 0 5 i 2 Becke 3 parameter parameters from ref 27 i 3 Becke 1998 B98 i 4 Schmider and Becke 1998 SB98 i 5 Becke 1997 reparametrized B97 1 If the value of i in idft is 1 or 2 the functionals given by j k I and m are combined using coef ficients determined by the appropriate hybrid method as indicated in Table 9 14 For the half amp half hybrids half of the exact exchange is automatically included with half of the selected exchange functional The coefficient of any local correlation functional or non local exchange or correlation functional is also set to 0 5 You must specify a Slater or Xo local exchange functional for a half amp half hybrid and if you use the Lee Yang Parr functional you may not specify a local correlation functional For Becke 3 parameter
439. py when degenerate sites are present This correction can be applied manually as needed after the 1 and 2 correction factors have been automatically applied by Jag uar see Section 14 2 2 on page 314 332 Jaguar 6 0 User Manual Chapter 15 Getting Help Schr dinger software is distributed with documentation in PDF format If the documentation is not installed in SCHRODINGER docs on a computer that you have access to you should install it or ask your system administrator to install it For help installing and setting up licenses for Schr dinger software and installing documenta tion see the Schr dinger Product Installation Guide Maestro has automatic context sensitive help Auto Help and Balloon Help or tooltips and an online help system To get help follow the steps below Check the Auto Help text box which is located at the foot of the main window If help is available for the task you are performing it is automatically displayed there Auto Help contains a single line of information For more detailed information use the online help If you want information about a GUI element such as a button or option there may be Balloon Help for the item Pause the cursor over the element If the Balloon Help does not appear check that Show Balloon Help is selected in the Help menu of the main win dow If there is Balloon Help for the element it appears within a few seconds For information about a panel or the
440. r HOSTS The hosts listed are those in the schrodinger hosts file that are being used by the jaguar command If you find that the list of hosts is incomplete you may need to edit the schrodinger hosts file indicated on the first line of the command output See Section 11 1 on page 269 for a description of the schrodinger hosts file 11 2 2 Selecting Particular Jaguar Executables By default Jaguar looks for the executables available for the machine upon which you want to run a Jaguar job then uses the most recent Jaguar executables for that machine type However if you have several differing sets of Jaguar executables at your site such as different versions of Jaguar or executables for different machine types you can choose to run your Jaguar job with a non default choice of executables To determine which sets of Jaguar executables are available enter the command jaguar LIST to find out about executables on the current host or jaguar LIST HOST hostname to find out about executables on another machine 11 2 8 Running a Jaguar Job From the Command Line The jaguar run command lets you run a Jaguar job using the Jaguar input file you specify and any of the jaguar run command options shown in Table 11 4 and described below The first Jaguar 6 0 User Manual 275 Chapter 11 Running Jobs Table 11 4 Options for the jaguar run command Option Effect Default Behavior HOST Run a Jaguar job on the specified host or Run
441. r Input File Table 9 30 Keywords related to localization of orbitals Continued Keyword Value Description locpostv 0 Do not localize valence orbitals of final wave function 1 Perform Boys localization on valence orbitals of final wave function 2 Perform Pipek Mezey localization on valence orbitals of final wave function maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals of final wave function maximizing Mulliken basis function populations iordboy 0 Do not order orbitals at end of Boys localization 1 Order orbitals by their one electron energy at the end of Boys localiza tion ixtrboy 0 Do not try to diagonalize multiple bond orbitals at the end of the Boys localization 1 Try to diagonalize multiple bond orbitals at the end of the Boys local ization see text in this subsection 9 5 19 File Format Conversion Keywords You can call the program Babel 24 from Jaguar to generate files in any of a variety of formats although the files produced by Babel contain only geometries not calculation settings The output can be generated at the end of each iteration in a geometry optimization or at the end of any job To generate such an output file you must set the format keyword for the chosen file type The format keywords and file types supported are shown in Table 9 31 If you want to generate an output file in a particular format only at the end of a job you should use a keyword
442. r currently cannot use g or higher basis functions basis functions with angular momentum g or higher are removed from the basis set and a warning is displayed If a basis set contains an ECP with h or higher potential projectors with angular momentum g or higher the entire basis set for that element is not converted and a warning is displayed The reason for discarding the entire basis set is that the ECP is not valid for molecular calculations if some projectors are removed from the ECP The script does not automatically distinguish polarization or diffuse functions from regular basis functions If polarization or diffuse functions are included in the basis set and you want to be able to select them by using or then you must edit the output from the script and add the appropriate data to mark the basis function as a polarization or a diffuse function as described on page 244 Otherwise Jaguar treats them as part of the standard basis set as it does for cc pVTZ for example Note Any basis sets you add will only be available for non pseudospectral calculations because they do not have associated grids and dealiasing functions 10 2 The Initial Guess Data File The file default atomig contains the results of Hartree Fock calculations on atoms for various basis sets By default the initial guess is constructed from wave functions in this file When the basis set to be used for the calculation is 6 31G MSV LAV2P LAV2D LAV3P
443. r geometry input and set all rele vant bonds equal to the same variable See Section 3 4 4 on page 37 and Section 3 4 6 on page 40 for more information 4 7 GVB LMP2 Settings Jaguar s pseudospectral GVB LMP2 module allows this multireference perturbation method to be applied to medium and large molecules with reasonable CPU memory and disk use The method has been shown to give highly accurate conformational energies 18 For GVB LMP calculations Jaguar first performs an SCF calculation of the reference GVB wave function using the GVB pairs specified in the input Next the program applies an LMP2 perturbative correction to the energy The LMP2 calculation is performed on the entire system even if only part of the system was treated at the GVB level To set up a GVB LMP2 calculation choose GVB LMP2 from the Level of theory option menu in the Theory folder The calculation is performed on all atom pairs If you want to restrict the atom pairs used you must edit the input file and add the appropriate keywords You can control the localization of the orbitals and the delocalization due to resonance just as for Hartree Fock based LMP2 calculations see Section 4 5 on page 63 We advise using GVB LMP2 primarily for single point energy calculations since Jaguar cannot compute GVB LMP2 atomic charges or analytic gradients For best results with GVB LMP 2 first run your calculations with the 6 31G basis set then change the basis set in the
444. r optimization including any from coord or connect sections if they exist 2 Use internal coordinates from input Z matrix for optimization note if geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom intopt is reset to 1 nmder 0 If calculating forces compute analytic derivatives of energy 1 If calculating forces compute numerical derivatives of energy obtained from calculations on 6 N om perturbed geometries by moving each atom pertnd bohr in positive or negative x y or z direction 2 Calculate frequencies numerically needgwd 0 Do not compute DFT grid weight derivatives 1 Compute DFT grid weight derivatives and second derivatives if using CPHF 2 Compute DFT grid weight derivatives and gradient from grid translation symmetry will be turned off 3 Compute DFT grid weight derivatives and gradient from grid translation and rotation symmetry will be turned off maxitg gt 0 Maximum number of optimization iterations maximum number of structures generated default is 100 iaccg 2 Use default convergence criteria shown in Table 9 21 3 Perform quicker coarser calculation by multiplying convergence criteria shown in Table 9 21 by 5 4 Solution phase criteria a factor of 3 times the criteria shown in Table 9 21 nogdiis 0 Use GDIIS method Geometry optimization by Direct Inversion in the Iterative Subspace 123 to get new geometry 1 Don t use G
445. r uie teque 271 entries in schrodinger hosts 271 listing available ess 275 Index SElECUB goce aic 48 277 troubleshooting ess 293 294 execution path 239 241 F field electric input file section for 237 file VO directory etin file names sssesessseeeeeeeeee nennen file output keywords filters project entry eene first shell correction factor for solvation keyword fixed entries Fock matrix in DIIS error vector 114 143 keywords for output of 213 216 new estimate from DIIS scheme 113 143 pseudospectral assembly of 155 157 upda ng eie updating keyword forces keywords formal charge rtr tte fragments building structures from 18 defining nocere estate 233 frequencies for 200 234 fred Program iin ee 240 frequencies ined Eire enit 79 84 ANALYTIC isseire tette 79 fragment nessis riesen 200 234 key words eerte ttn 189 199 QUEDUE m 129 131 Scaling zerrissen 80 81 visualizing in Maestro visualizing with Molden frequency related properties IKE YW OPUS cidit ert t 199 Maestro settings esee 83 84 OUEDUE us senken 129 131 function key macros see scripts functionals see
446. ram scf takes the initial orbitals and iteratively modifies them with the pseudospectral method until convergence This process involves calculating the values of the necessary integrals on the grid points and actually assembling the Fock matrix from the computed information The three center one electron pseudospectral integrals on the grid points are defined by 9 1 0 1 E Fr r Q Pis Ig where and are basis functions and the index g represents a grid point These integrals are calculated for all combinations of basis functions and grid points not eliminated by cutoffs and the Fock matrix is assembled from its Coulomb and exchange matrix components J i and K j which are calculated in physical space and transformed back into spectral space by the following equations Jij m Yel Y Au Du R 3a g kl Kj X04 Dina Panne 3b g n m where D is the usual spectral space density matrix R is the value of the function j at grid point g and A klg is given by Equation 2 The grid points used for each SCF iteration are Jaguar 6 0 User Manual Chapter 8 Theory determined by the grid type coarse medium fine or ultrafine chosen for that iteration The number of arithmetic operations involved in the assembly of the matrices J and K in Equation 3a and Equation 3b scales formally as N as opposed to the N scaling for the matrix assembly in the conventional spectral space algorithm Jaguar actually uses the pseudospe
447. rb orbitals left Setting ncanorb sets icanorb to a positive value Jaguar 6 0 User Manual 205 Chapter 9 The Jaguar Input File 206 9 5 17 Initial Guess Keywords Table 9 29 lists the keywords related to the initial guess and the meaning of the values each keyword can take on Most of the keyword values in Table 9 29 correspond to options described in Section 4 8 on page 68 Table 9 29 Initial guess keywords Keyword Value Description igonly 0 1 No effect Use initial guess or input wave function for any post SCF calculations skipping SCF step No J K or Fock matrices are created therefore properties that require any of these matrices cannot be calculated iguess 0 10 11 25 30 Generate initial guess by diagonalizing one electron Hamiltonian Read initial guess from guess section from input file or from guess file specified in WAVEFNFILE line iguess 1 automatically if input file contains non empty guess section Construct initial guess from orbitals which give best overlap with atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atoms note that if guess section exists this is not the default choice Construct initial guess from orbitals whose densities when summed best agree with the sum of the densities of the atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atom
448. rces However it cannot be read into Maestro as it is You can use the UNIX command csplit to break up the jobname steps in file into individual input files any of which can then be modified and submitted to Jaguar Each input section in the jobname steps in file terminates with the string END OF INPUT You can use this string to tell csplit where to split the file For example for a jobname steps in file that has 3 input sections in it the command csplit prefix jobname jobname steps in END OF INPUT creates four files called jobname00 jobname01 jobname02 and jobname03 the last of which contains the last END OF INPUT string and can be deleted After renaming these files so that they have a in extension they can be use as Jaguar input files All but the first file contain the END OF INPUT string which Jaguar treats as a comment See the UNIX man page for csplit for more information man csplit 5 5 Intrinsic Reaction Coordinate Calculations Intrinsic Reaction Coordinate IRC calculations can be used to check that the given transition state is the expected transition state for the reaction of interest IRC calculations start at a tran sition state and move downhill in energy along the reaction path toward a minimum of the potential energy surface calculating a series of points in which all geometric variables orthog onal to the path are optimized The calculations can run in the forward direction toward the products
449. re removed when you close the dialog box 3 4 Molecular Structure Input After you start Maestro the first task for setting up any Jaguar calculation is to enter a molec ular structure geometry You can create a structure using Maestro s Build panel you can use the Jaguar panel to read in a file as described in Section 3 5 on page 41 or you can enter and edit the geometry yourself in Cartesian x y z coordinates or in Z matrix format using the Edit Job dialog box This section describes the input formats for Cartesian and Z matrix geom etries The geometry input is used to set constraints of bond lengths or angles for geometry optimization and to specify atoms for a counterpoise calculation These aspects of geometry input are explained in this section as well The geometries that you enter are displayed in the Workspace in which you can rotate and translate the structure change the geometry display in various representations and perform many other tasks For information on Maestro see Chapter 2 or the Maestro User Manual 1 The geometry input is in the zmat and zvar sections of the input file Jaguar 6 0 User Manual 35 Chapter 3 Running Jaguar From Maestro 36 3 4 4 Cartesian Format for Geometry Input The Cartesian geometry input format can consist of a simple list of atom labels and the atomic coordinates in angstroms in Cartesian x y z form For example the input Oo 0 000000 0 000000 0 113502 H1 0
450. rect dissociation behavior for a sigma bond Jaguar 6 0 User Manual 207 Chapter 9 The Jaguar Input File 208 In the transition metal initial guess section tmig Jaguar generates a set of states with all possible d orbital occupations You can select one of these states by setting istate to the state index This capability is useful when there are degenerate states such as in highly symmetric transition metal complexes When degenerate states are encountered Jaguar prints a warning message that lists the states with a state index number and by default continues the calculation with the first state This calculation might not converge to the ground state so you should run calculations for each state to determine which is the desired state To run a calculation with another state set istate to the state index number listed in the output 9 5 18 Localization Keywords For any Jaguar job the final wave function can be localized after it is computed Localization can also be used to provide localized orbitals for the LMP2 method see Section 9 5 6 on page 178 for details The keywords in Table 9 30 describe the available options for final wave function localization See Section 4 8 4 on page 71 for a description of the localization methods and the GUI settings related to localization When the keyword ixtrboy described in Table 9 30 is set to 1 an additional procedure is added on to the Boys localization process Boys orbitals may b
451. ree Fock wave functions DFT calculations are selected by choosing DFT Density Functional Theory from the Level of theory option menu in the Theory folder When you make this choice controls for DFT calcu lation are displayed below this menu If you are doing calculations for an open shell molecule you can run a spin restricted RODFT or a spin unrestricted UDFT calculation The default is a spin restricted calcula tion To run a UDFT calculation select Spin unrestricted The Grid density menu determines the grid for DFT calculations By default DFT calculations use grids with a medium point density but finer density grids are also available You can choose between Medium Fine or Maximum grid density If you read an input file that contained some other grid density the grid density is set to Other otherwise this option is unavailable If you choose a grid density from this menu the previous grid density specifica tion is replaced Keyword iuhf 0 in the gen section Keyword iuhf 1 in the gen section Keywords gdftmed 10 gdftfine 11 and gdftgrad 12 in the gen section Keywords gdftmed gdftfine and gdftgrad 13 in the gen section Keywords gdftmed gdftfine gdftgrad 14 in the gen section ER Jaguar 6 0 User Manual 59 Chapter 4 Options 60 Jaguar jaguar Haki Use structures from Workspace included entries 1 Molecule Theory scF Properties Solvation Outp
452. relation functional 30 Gradient Corrected Pure Density Functionals BLYP Exchange Slater local functional 29 Becke 1988 nonlocal gradient correction 32 correlation Lee Yang Parr local and nonlocal functionals 33 BPwo91 5 Exchange Slater local functional 29 Becke 1988 nonlocal gradient correc tion 32 correlation Perdew Wang 1991 GGA II local and nonlocal functionals 31 BP86 6 Exchange Slater local functional 29 Becke 1988 non local gradient correction 32 correlation Perdew Zunger 1981 local functional 34 Perdew 1986 gradient cor rection functional 35 BP86 VWN5 Exchange Slater local functional 29 Becke 1988 nonlocal gradient cor rection 32 correlation Vosko Wilk Nusair VWN local functional 30 Perdew 1986 gradient correction functional 35 PwPwo1 8 Exchange Slater local functional 29 Perdew Wang 1991 gradient correc tion functional 31 correlation Perdew Wang 1991 GGA II local and nonlocal func tionals 31 PBE Perdew Burke Ernzerhof local and nonlocal exchange and correlation functional 41 10 11 12 13 14 15 16 17 18 19 Keyword dftname hfs in the gen section Keyword dftname xalpha in the gen section Keyword dftname svwn in the gen section Keyword dftname svwn5 in the gen section Keyword dftname blyp in the gen section Keyword dftname bpw91 in the gen section Keyword dftname bp86 in the gen section Keyword dftname bp8
453. ring a geometry through the GUI can be found in Section 3 3 on page 34 and Section 3 4 on page 35 The units for the geometry are set by the iunit keyword of the gen section by default these units are angstroms and degrees If the geometry is in Cartesian coordinates each line must contain four items an atom name and the x y z coordinates Each item should have at most 80 characters The atomic label should begin with the one or two letter elemental symbol in either uppercase or lowercase characters Additional alphanumeric characters may be added as long as the atomic symbol remains clear for instance HE5 would be interpreted as helium atom 5 not hydrogen atom ES Up to eight characters can be given in an atomic label A sample Cartesian zmat section for a water molecule is amp zmat O 0 000000 0 000000 0 113502 H1 0 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 amp A zmat section in Z matrix format should not include lines defining variables which are set in the zvar section described in Section 9 3 on page 171 and should not contain any comment lines but otherwise should have the same format as described in Section 3 4 4 Section 3 4 5 and Section 3 4 6 Section 3 4 6 also includes a description of how to specify bond length or angle constraints on the Z matrix coordinates for geometry optimizations You can orient the molecule or system using a label on the same line as the zmat section label This orientati
454. ring by the United States Government or the University of California The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or the University of California and shall not be used for advertising or product endorsement purposes Maestro 7 0 User Manual References The first 18 references listed below provide general information about the algorithms used in Jaguar and some of their applications Their titles are included in the listings and copies of some of these references are available from Schr dinger upon request The other listings in this section are referenced throughout this manual 1 10 11 Friesner R A Solution of Self Consistent Field Electronic Structure Equations by a Pseudospectral Method Chem Phys Lett 1985 116 39 Friesner R A Solution of the Hartree Fock equations by a pseudospectral method Application to diatomic molecules J Chem Phys 1986 85 1462 Friesner R A Solution of the Hartree Fock equations for polyatomic molecules by a pseudospectral method J Chem Phys 1987 86 3522 Friesner R A An Automatic Grid Generation Scheme for Pseudospectral Self Consis tent Field Calculations on Polyatomic Molecules J Phys Chem 1988 92 3091 Ringnalda M N Won Y Friesner R A Pseudospectral Hartree Fock calculations on glycine J Chem Phys 1990 92 1163 Langlois J M Muller R P Coley T
455. rrelation methods used in Jaguar This chapter includes information on pseudospectral Jaguar 6 0 User Manual Chapter 1 Introduction implementations of GVB and local MP2 techniques and a brief description of density func tional theory Chapter 9 describes the Jaguar input file in detail You may find this chapter especially useful if you want to run some jobs without using the GUI Chapter 10 describes other Jaguar files that are necessary for calculations You may skip Chapter 9 and Chapter 10 if you want to run all jobs from the GUI but you might want to skim them anyway to find out more about Jaguar and the methods it uses Chapter 11 provides information on configuring hosts the environment and the Schr dinger software to run Jaguar submitting jobs from the command line and running multiple Jaguar jobs using batch scripts Chapter 12 contains troubleshooting hints concerning various problems you might encounter especially when first setting up Jaguar on your system Chapter 13 contains information on running calculations on parallel computers Chapter 14 describes the pKa calculation module Citing Jaguar in Publications The use of this product should be acknowledged in publications as Jaguar version 6 0 Schr dinger LLC New York NY 2005 Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro Maestro is the graphical user interface for all of Schr dinger s products FirstDiscovery Glide Imp
456. rs which identify the number of orientations of a molecule which can be obtained from each other by rotation and zero point energies are also computed You can calculate these properties only if you are also computing vibrational frequencies With the settings in the Thermochemistry section you can set the temperatures and the pres sure used for calculations of these quantities The pressure in atm used for thermochemical calculations is 1 0 by default and the initial temperature in K is 298 15 by default To compute thermochemical properties at more than one temperature specify the differences between temperatures using the Increment text box and the number of temperatures at which 88 Keyword irder 1 in the gen section 89 Keyword press in the gen section 90 Keyword tmpini in the gen section Jaguar 6 0 User Manual 83 Chapter 4 Options 84 to compute thermochemical properties in the Number of steps text box The defaults are 10 00 K and 1 step meaning only one temperature is used By default thermochemical output is in units of kcal mol for H and G and cal mol K for C and S For output in units of kJ mol and J mol K instead select kJ mol under Output 4 12 Surfaces By selecting Surfaces MO density potential in the Properties folder you can generate elec trostatic potential electron density electron spin density and orbital data that can be visualized using the surfa
457. run executes a Python module You can also use the alias pyrun The syntax is pythonrun module function pythonimport tereads a Python file so that the next time you use the pythonrun com mand it uses the updated version of the module You can also use the alias pyimp From the Maestro Scripts menu you can install manage and run Python scripts For more information on the Scripts menu see Section 12 1 of the Maestro User Manual Jaguar 6 0 User Manual 23 Chapter 2 Introduction to Maestro 24 For more information on using Python with Maestro see the Python tutorial located in SSCHRODINGI 2 7 2 ER docs python tutorial py23 tutorial Command Scripts All Maestro commands are logged and displayed in the Command Script Editor panel This means you can create a command script by performing the operations with the GUI controls copying the logged commands from the Command History list into the Script text area of the panel then saving the list of copied commands as a script To run an existing command script 1 Open the Command Script Editor panel from the Edit menu in the main window 2 Click Open Local and navigate to the directory containing the desired script 3 Select a script in the Files list and click Open The script is loaded into the Script window of the Command Script Editor panel 4 Click Run Script Command scripts cannot be used for Prime operations The Command Histo
458. run with input files that vary only in the value of one or more variables used to define an internal or Cartesian coordinate in the input structure You can perform a relaxed scan finding minimum energy geometries while holding one or more coordinates fixed to various values or a rigid scan varying only the scan coordinates To scan over a coordinate you must first define the coordinate as a variable then define the values that the coordinate must take You can set up geometry scans from Maestro or you can create an input file with the appropriate sections 28 Keyword nhesref 3 in the gen section Jaguar 6 0 User Manual Chapter 5 Optimizations and Scans Jaguar jaguar Silex Use structures from Workspace included entries 1 Molecule Theory scr Optimization Scan Properties Solvation Output Add new coordinate Type Distance F Pick Atoms Defined coordinates maximum of 5 Coordinate r Selected coordinate Cine u Distanc Current value Starting value Final value Total number of structures to be calculated 21 Increment Number of steps 54 Delete Job blyp 6 31G Relaxed Coordinate Scan Start Read Write Edit Reset Close Help Figure 5 3 The Scan folder 5 4 1 Setting up Scans in Maestro To set up a scan from Maestro choose Relaxed coordinate scan or Rigid coordinate scan from the Jaguar submenu of t
459. ry window displays a log of all commands issued internally within Maestro when you interact with a panel menu or structure Command Script Editor script Command History organic Carbonyl organic Methul Opens the Show Hide Command panel used to determine which commands are Select All Deselect All Show Hide Copy Selection To Script 3i W Log commands logged in the grow fragment organic Methy Command His frag tory list fragment organic Methy grow fragment organic Carbonyl grow fragment organic Methy1 grow d Run Script Sox 3 Open Local Open Global Save As EP Expand Command Aliases Close Help Figure 2 5 The Command Script Editor panel Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro 2 7 3 Macros There are two kinds of macros you can create named macros and macros assigned to function keys F1 through F12 To create and run a named macro 1 Open the Macros panel from the Edit menu in the main window 2 Click New enter a name for the macro and click OK 3 In the Definition text box type the commands for the macro 4 Click Update to update the macro definition 5 To run the macro enter the following in the command input area in the main window macrorun macro name If the command input area is not visible choose Command Input Area from the Display menu To create and run a function key macro 1 Open the Function Key Ma
460. s 145 146 147 148 149 150 Langlois J M Ph D Dissertation California Institute of Technology Pasadena CA 1994 Perez Jorda J M Becke A D San Fabian E J Chem Phys 1994 100 6520 Baker J Andzelm J Scheiner A Delley B J Chem Phys 1994 101 8894 Mura M E Knowles P J J Chem Phys 1996 104 9848 Gonzalez C Schlegel H B J Chem Phys 1989 90 2154 J Chem Phys 1990 94 5523 Klicic J J Friesner R A Liu S Y Guida W C J Phys Chem A 2002 106 1327 Jaguar 6 0 User Manual 343 References 344 Jaguar 6 0 User Manual Index A accuracy level 68 88 Keyword cech eie He 202 accurate energetics nossen sese 52 acidic site designating for pK calculations 327 AIMPAC w n file keyword 215 all analytic calculation keyword 203 analytic gradient of energy 89 convergence criteria esee 89 keywords eerte 186 191 analytic integral corrections keyWord HE nee 203 specifying in cutoff file 259 THEORY oceani oninia dins 157 angles see bond angles antiferromagnetic systems 148 234 atom labels format usa 36 37 170 In Output i5 cin ore ettet arent 110 orbital output sene 141 217 atomic charges see charges atomic atomic masses for frequency calculations 79 ke
461. s For a system that contains transition metal atoms construct a high quality initial guess using ligand field theory as described in reference 19 Not available for GVB calculations For a system that contains transition metal atoms construct a high quality initial guess using ligand field theory including d d repulsion as described in reference 19 Not available for GVB calculations ihfgvb 0 Jaguar 6 0 User Manual a Read in GVB initial guess from guess section if iguess 1 and do not run hfig or gvbig programs or b Compute it from HF initial guess whose origin is determined by iguess if iguess 1 Converge HF wave function where the initial guess is determined by iguess and use converged HF wave function as input to program gvbig to get GVB initial guess Calculate a GVB initial guess from HF initial guess whose origin is determined by setting iguess Chapter 9 The Jaguar Input File Table 9 29 Initial guess keywords Continued Keyword Value Description ihamtyp 0 Construct Hamiltonian using standard core open and GVB orbitals 2 Make highest two orbitals in initial guess an open shell singlet pair ROHF only 3 Input Hamiltonian in ham section ihamtyp 3 by default if a non empty ham section exists ioss 0 Use the default open shell guess 1 Set up an open shell singlet initial guess by mixing the LUMO into the HOMO and set isymm 0 and iuhf 1 See text istate 0 Use the default state select
462. s 1980 58 1200 The VWN correlation functional is described in the paragraph below equation 4 4 on p 1207 while the VWNS functional is described in the caption of Table 5 and on p 1209 Perdew J P In Electronic Structure Theory of Solids Ziesche P Eschrig H Eds Akademie Verlag Berlin 1991 Perdew J P Chevary J A Vosko S H Jackson K A Pederson M R Singh D J Fiolhais C Phys Rev B 1992 46 6671 Becke A D Phys Rev A 1988 36 3098 Lee C Yang W Parr R G Phys Rev B 1988 37 785 implemented as described in Miehlich B Savin A Stoll H Preuss H Chem Phys Lett 1989 157 200 Perdew J P Zunger A Phys Rev B 1981 23 5048 Perdew J P Phys Rev B 1986 33 8822 and Perdew J P Phys Rev B Erratum 1986 34 7406 Becke A D J Chem Phys 1997 107 8554 Becke A D J Chem Phys 1998 109 2092 Schmider H L Becke A J Chem Phys 1998 109 8188 Schmider H L Becke A J Chem Phys 1998 108 9624 Hamprecht F A Cohen A J Tozer D J Handy N C J Chem Phys 1998 109 6264 Boese A D Handy N C J Chem Phys 2001 114 5497 Jaguar 6 0 User Manual 337 References 338 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Perdew J P Burke K Ernzerhof M Phys Rev Lett 1996 77 3865 Phys Rev Lett Erratum 1997 78 1386
463. s including multipole moments and charge fitting properties are listed in Table 9 25 most of which correspond to GUI options described in Section 4 10 on page 74 Only the values listed in the table are allowed Table 9 25 Keywords for charge fitting multipole moment and polarizability and hyperpolariz ability calculations Keyword Value Description icfit 0 Do not do electrostatic potential fitting 1 Fit electrostatic potential to atomic centers default for solvation cal culations 2 Fit electrostatic potential to atomic centers and bond midpoints cfiterr 1 0x10 Allowed error in electrostatic potential charge fitting when fitting is constrained to reproduce multipole moments wispc 0 75 Spacing in bohrs of rectangular grid for electrostatic potential fitting incdip 0 Use only total charge as constraint in electrostatic potential fitting 1 Use charge and dipole moment as constraints in electrostatic potential ESP fitting 11 Use charge dipole moment and quadrupole moment as constraints in electrostatic potential ESP fitting 111 Use charge dipole moment quadrupole moment and octupole moment as constraints in electrostatic potential ESP fitting ijk Compute ESP fitted charges using total charge as a constraint also constraining to dipole moment if k 1 to quadrupole moment if j 1 and to octupole moment if i 1 1 Do all incdip options sequentially Idips Do not calculate any multipole moments Calculate di
464. s instructions for batch queue configuration No information on batch queue configuration is given in this chapter Maestro searches the following directories for a schrodinger hosts file in the order given and uses the first one that it finds The directory in which you started Maestro SHOME schrodinger SSCHRODINGER You can always determine which schrodinger hosts file is being used by entering the following command in the directory in which you started Maestro SSCHRODINGER jaguar HOSTS Jaguar 6 0 User Manual 269 Chapter 11 Running Jobs The location of the schrodinger hosts file is the first output line of this command If you want to change entries in the schrodinger hosts file you should copy and edit your own schrodinger hosts file If there is no schrodinger hosts file in your HOME Schrodinger directory or the directory from which you start Maestro you should identify the schrodinger hosts configuration file currently used by Maestro copy this schrodinger hosts file to your HOME schrodinger directory or the directory where you want to start Maestro and edit it there The following is an example of a schrodinger hosts file Schrodinger hosts file name localhost schrodinger software schrodinger name ahost name bhost name old_bhost host bhost schrodinger software schrodinger_old name another_host processors 2 tmpdir ser schrodinger usr bin
465. s 198 apr 84 electrostatic potential fitting 74 76 constraining to reproduce multipole MOMENUS ET 74 for LMP2 wavefunctions 74 for solvation calculations 71 120 121 STI for 75 76 keywords esnan e 196 keywords for grid 196 220 OUtput MTOM agenais 175 recalculating multipole moments from 75 76 RMS error in output 125 setting options for 74 energy components keyword for output of 216 energy convergence criterion nenne 69 keyword for its 201 energy difference as geometry convergence criterion 89 119 keyword for geometry convergence 191 energy output final GVB components 116 final SCF components 114 SCF components for each iteration 216 SOLVALION sssisesedsssssisiastivrvessesussaserveioee total SCF for each iteration z two electron contributions 135 enthalpy calculations entries Project Table including excluding and fixing sa L5 SCIECHNE seen is ls po m 13 entropy calculations 83 84 130 200 environment variables DISPLAY 4 291 Jaguar 6 0 User Manual iz 9j o 304 JAGUAR EXHBG iiiertesstssestebkeet ete eut eotnus 303 JAGUAR SCRATCH 272 LD_LIBRARY_PATH nn 303 MMSHARE EXEC nike 303 MP HOSTFILE eere 305 MP
466. s below amp path path executable list amp More complicated paths involve looping over programs until the last Jaguar program in the loop indicates that convergence is reached The first program in the section of the path to be looped over is preceded by a loop label and the last is followed by a goto label where each of these labels is followed by the same character string Nested loops are also allowed The following path illustrates a loop which will cause the programs pre onee grid and ig to run once the series of programs rwr scf derla rwr der1b and geopt to run until the convergence criteria for geometry optimization are satisfied and the program post to run once amp path pre onee grid hfig loopal rwr scf derla rwr derlb geopt gotoal post amp If you put a jump label between a loop label and a goto label where jump is followed by the same character string that follows loop and goto jumpal for the above path for instance the path will jump to the end of the loop after the goto label and will exit the loop when the jump label indicates that the convergence criterion for that program is reached Note that since loops will only exit when convergence is reached the program before a goto or jump label must have such a criterion The three programs which can precede a goto or jump label are sc when it is being used for solvation runs g
467. s that all orbitals are to be printed in Fortran f8 5 format after the GVB initial guess is created The options ip105 12 are not valid use ip100 instead In canon ical orbital space the atom and function type labels are meaningless If a keyword is set to 4 5 9 or 10 the orbitals can be used for input in the guess section or for GAUSSIAN guess cards When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital is listed in turn with the function coefficients listed in order When ipx 2 n only coefficients larger than a particular value generally 05 are listed and the atom identifiers for instance h2 and function types for instance S for s Z for p are shown When ipx 4 n or ipx 5 n all coefficients are listed in order but without numbering For examples of the output that shows up in the output file for a calculation of water with a 6 31G basis set for various values of ip104 see the five examples given at the end of Jaguar 6 0 User Manual 217 Chapter 9 The Jaguar Input File 218 Section 6 6 on page 139 The five examples correspond to ip104 2 ip104 3 ip104 4 ip104 5 and ip104 6 in that order Only the first two occupied orbitals are shown in each case and not all functions are shown those gaps are indicated by 9 5 24 Grid and Dea
468. s the element symbol e g Na and two numbers The first number is the maximum angular momentum in the core and the second gives the number of electrons replaced by the effective core potential Next the infor mation for various angular projectors is listed The first set of information contains the local components of the ECP and should begin with a line starting D AND UP F AND UP Or G AND UP which indicates that the maximum angular momentum to be described is 2 3 or 4 Following that line the different terms for this angular projector are given Each line describes a term of the form Cew rn 2 listing the parameters n amp and C from left to right in a free format Next the angular projectors are listed in increasing order S P D etc in the same fashion A line with four characters appears the end of the description of each atom s ECP When all atoms have been described in turn the next basis set is described The example below shows the beginning of the description in default basis of the LAV2D and LAV2P basis sets Note that these basis sets only differ in their choice of what basis set to use for atoms that are not described by the effective core potential BASIS LAV2D LANL1DZ 5D ECP BACKUP D95V BASIS LAV2P 5D ECP BACKUP 6 31G Na S 0 d qud 0 497200000000000 0 275357400000000 5 600000000000000E 02 1 09899690000000 S 0 i 9 2 210000000000000E 02 1 00000000000000 P 0 Kas ea pou 0 6
469. s the types of grids that can be specified for portions of the calculation that do not involve density functional theory Generally these grid types are used for pseudospectral SCF iterations or for charge fitting Table 9 37 Pseudospectral charge fitting and electron density grid types Name Description coarse Least expensive least accurate level medium Used for most SCF iterations fine Sometimes used for a limited number of iterations ufine Ultrafine most accurate level grad Used in gradient computation Imp2 Grid used for LMP2 energy calculations Imp2grad Grid used for LMP2 gradient calculations charge Grid used for charge fitting eldens Used for electron density calculations a These names are used in the grid related keywords described in Table 9 38 The grid related keywords and their allowed and default values are given in Table 9 38 where name corresponds to one of the grid types listed in Table 9 37 As an example gmedium 2 indicates that the medium grid to be used is the second one listed in the grid file while geldens 3 indicates that an electron density calculation should use a cubic grid You can read in your own set of grid points and weights by using the gname 6 option and the GPTSFILE line of the input file which is described in Section 9 1 on page 167 9 5 25 Memory Use Keywords Some of the memory use for Jaguar can be controlled through keywords These keywords may be particularly useful if y
470. save the filter for future use click Create Filter enter a name and click OK 5 Click OK to apply the filter immediately 2 4 4 Including Entries in the Workspace In addition to selecting entries you can also use the Project Table to control which entries are displayed in the Workspace An entry that is displayed in the Workspace is included in the Workspace likewise an entry that is not displayed is excluded Included entries are marked by an X in the diamond in the In column excluded entries are marked by an empty diamond Entry inclusion is completely independent of entry selection Jaguar 6 0 User Manual Chapter 2 Introduction to Maestro 16 To include or exclude entries click shift click or control click in the In column of the entries or select entries and choose Include or Exclude from the Entry menu Inclusion with the mouse works just like selection when you include an entry by clicking all other entries are excluded It is sometimes useful to keep one entry in the Workspace and include others one by one for example a receptor and a set of ligands You can fix the receptor in the Workspace by selecting it in the Project Table and choosing Fix from the Entry menu or by pressing CTRL F A padlock icon replaces the diamond in the In column to denote a fixed entry To remove a fixed entry from the Workspace you must exclude it explicitly CTRL X It is not affected by the inclusion or exclusion of other entries F
471. schrodinger hosts file in the directory where Jaguar was installed and list in it the names of the hosts in the machines LINUX file The host names in schrodinger hosts need not include the domain name See Section 11 1 on page 269 for details on the format of the schrodinger hosts file For the above example the schrodinger hosts file would look like host homer schrodinger apps Schrodinger tmpdir ser Jaguar 6 0 User Manual 299 Chapter 13 Parallel Jaguar 300 processors 2 I host marge schrodinger apps Schrodinger tmpdir ser processors 2 I host bart schrodinger apps Schrodinger tmpdir ser processors 1 4 Ensure that rsh is enabled By default Jaguar uses rsh to communicate with remote nodes even if you are running on a stand alone SMP workstation with 2 CPUs To enable rsh each user must create a file called rhosts in his or her home directory The rhosts file should contain the name of each host listed in the file machines LINUX followed by the user s login name e g homer mynet edu username marge mynet edu username bart mynet edu username The rhosts file must be owned by the user not by root and must not be writable by anyone except the user or authentication fails To ensure this enter the command chmod 644 rhosts We strongly recommend that you test rsh connections by using the shell script tstmachines which is in MPICH install sbin This script attempts to run
472. section Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files The distances defining the neighbor ranges are set in the next line of real values in units of bohr Note however that generally only the third neighbor range is actually used The first distance specifies that if the basis function whose coefficient is being evaluated is to be approx imated by short range dealiasing functions then the dealiasing functions for first order neigh bors will be used for each atom within this distance of the atom upon which the basis function is centered except for the basis function atom itself for which the home atom dealiasing func tions will be used The second distance defines which atoms are considered second order neighbors to each other and so on Since the number of neighbor ranges includes not only these ranges but also the long range over the entire molecule and the home atom range consisting of the relevant atom itself the number of neighbor ranges actually specified in this line of the daf file should be two less than the number of ranges listed in the previous line Thus in the sample file the distances listed specify the neighbor ranges for first through fourth order neighbors The rest of the daf file contains the dealiasing function sets for each atom type within each basis set The data for each basis set should begin with a line listing the basis set name as listed in Table 4 1 on page 56 and Table 4 2 on page 58 inclu
473. see Section 3 9 of the Jaguar Quick Start Guide 31 Keyword iremode in the gen section 32 Keyword iremode downhill in the gen section 33 Keyword iremax in the gen section 34 Keyword irestep in the gen section 35 Keyword iremxcye in the gen section 36 Keyword irc 2 in the gen section 37 Keyword irc 1 in the gen section Jaguar 6 0 User Manual Chapter 6 Output The output from a Jaguar run always includes a Jaguar output file which contains the primary output a log file which contains a job summary that is updated as the job is being run and a Maestro formatted file which contains the geometry and properties in a form that can be read by Maestro and other Schr dinger software If you request other output options in the Output folder of the Jaguar panel various other files can also be generated as output This chapter begins with a description of the jaguar results utility which can be used to obtain summaries of Jaguar results The chapter continues with a description of the Jaguar output file for a standard Hartree Fock calculation followed by a discussion of the changes in the output for various other calculation options and the output options that can be set in the Output folder The final section explains the log file which is the file displayed in the Monitor panel as a job runs Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that correspond to particular GUI s
474. ses 292 12 1 5 Problems Running Jaguar Calculations on Other Nodes 293 12 2 Other Problems va ace end aan 294 Chapter 13 Parallel again 297 13 1 Installing Parallel Jaguar 13 151 S Gl Installatiori soit te 13 1 2 LINUX Installation 19 1 2 1 Installing MPICH aa sea rl 299 LE esee epic uses nee 299 13 1 2 3 Launching the Secure ServersS nuuuunssnnnnennennnnnenennnnnnnnnnnnnen nennen 300 19 1 2 4 Selecting Nodes for a JOD ota sen er 303 13 1 2 5 Troubleshooting Parallel Job Problems eene 303 13 1 3 IBM Installallohi iii oci eet ete oce tutes ei ee lud 304 13 2 Running Jobs in Parallel eseeeeeeeeeneennnnnn 306 Chapter 14 The pK Prediction Module 309 14 1 Theory of pK Calculation sse 310 14 1 1 Ab initio Quantum Chemical Calculation of pK Values 310 14 122 Empirical Corfeclionsz essen nase ERR Re Fa SPERARE E 312 Jaguar 6 0 User Manual xi Contents xii 14 2 Predicting pK Values in Complex Systems s 313 14 2 1 Conformational Flexibility 2 seen 313 14 2 2 Eguivalerit Sll8s ei inserieren 314 14 2 3 Multiple Protomation Sites ois nie li lu 315 14 3 Training Set Hesulls iieri aan 315 14 4 Running pK Calculations senes 325 14 4 1 Activating the pK Mo
475. setting of the form babel outext where outext is one of the possible format keywords listed in Table 9 31 You can set babel more than once using separate babel outext assignments if you want to generate several files To generate output files at the end of each iteration in an optimization set the babelg keyword to the appropriate output extension string Like the babel keyword the babelg keyword can be set more than once to generate files in several formats As files are generated with Babel during Jaguar runs they are immediately copied back to the relevant output directory Files generated from jobs with babel keyword settings have names of the form jobname outext for instance h20 spar where jobname is the usual job name and outext is the format keyword which is used as the output extension Files generated from geometry optimizations with babelg settings have names of the form jobnamef outext where is a four digit number corresponding to the iteration number for example 0001 for the first Jaguar 6 0 User Manual 209 Chapter 9 The Jaguar Input File 210 geometry iteration and all letters in the job name are converted to lower case by Babel Note that you can use a babelg keyword setting to write structures generated during an optimization as the optimization proceeds Table 9 31 Output format keywords and file types for babel file format conversions Format Keyword File Type alc Alchemy file bs B
476. shall the University or the Contributors be liable for any damages suffered by the users arising out of the use of this software even if advised of the possi bility of such damage Portions of HDF5 were developed with support from the University of California Lawrence Livermore National Laboratory UC LLNL The following statement applies to those portions of the product and must be retained in any redistribution of source code binaries documenta tion and or accompanying materials This work was partially produced at the University of California Lawrence Livermore National Laboratory UC LLNL under contract no W 7405 ENG 48 Contract 48 between the U S Department of Energy DOE and The Regents of the University of California University for the operation of UC LLNL DISCLAIMER This work was prepared as an account of work sponsored by an agency of the United States Government Neither the United States Government nor the University of Cali fornia nor any of their employees makes any warranty express or implied or assumes any liability or responsibility for the accuracy completeness or usefulness of any information apparatus product or process disclosed or represents that its use would not infringe privately owned rights Reference herein to any specific commercial products process or service by trade name trademark manufacturer or otherwise does not necessarily constitute or imply its endorsement recommendation or favo
477. share schrodinger End of Schrodinger hosts file The hosts file consists of one or more entries that describe a host on which jobs can be run Typically there will be a single entry for each machine on which you want to run jobs For each entry in the schrodinger hosts file the following settings can be made name entry label host machine name user userid tmpdir tempdir processors number of processors schrodinger installation path The settings are described in the following sections A full list of settings including settings for batch queue configuration is given in the Schr dinger Product Installation Guide 270 Jaguar 6 0 User Manual Chapter 11 Running Jobs A setting in the schrodinger hosts file can be formatted with any combination of spaces and tabs but the entire setting must be on one line Comments may be included in the schrodinger hosts file and should start with a hash sign If you have installed Jaguar on multiple machines you might need to edit the schrodinger hosts file on each machine to add entries for the other machines 11 1 1 The name and host Settings The name setting must be the first line for each entry This is the name that is displayed in the list of known hosts in the Host menu of the Start dialog box Usually entry label is the name of a machine a host that can be used to run a Jaguar calculation but if it is not you must include a host setting that supplies the mach
478. shnan R Binkley J S Seeger R Pople J A J Chem Phys 1980 72 650 McLean A D Chandler G S J Chem Phys 1980 72 5639 Mitin A V Baker J Pulay P J Chem Phys 2003 718 7775 Dunning T H Jr Hay P J Chapter 1 in Modern Theoretical Chemistry Methods of Electronic Structure Theory Schaefer H F III Ed Plenum New York 1977 Vol 3 Rapp A K Goddard W A Unpublished work Dunning T H Jr J Chem Phys 1989 90 1007 Kendall R A Dunning T H Jr Harrison R J J Chem Phys 1992 96 6796 Woon D E Dunning T H Jr J Chem Phys 1993 98 1358 Woon D E Dunning T H Jr J Chem Phys 1994 100 2975 Easton R E Giesen D J Welch A Cramer C J Truhlar D G Theor Chim Acta 1996 93 281 Thompson J D Winget P Truhlar D G Phys Chem Comm 2001 16 1 Li J Cramer C J Truhlar D G Theor Chem Acc 1998 99 192 Schafer A Huber C Ahlrichs R J Chem Phys 1994 100 5829 Hay P J Wadt W R J Chem Phys 1985 82 270 Hay P J Wadt W R J Chem Phys 1985 82 284 Hay P J Wadt W R J Chem Phys 1985 82 299 The LACV3P basis set is a triple zeta contraction of the LACVP basis set developed and tested at Schr dinger Inc Cundari T R Stevens W J J Chem Phys 1993 98 5555 Hurley M Pacios L F Christiansen P A Ross R B Ermler W C J Chem Phys 1986 54
479. should be used Alternatively you may leave the values blank for values at the end of the row For instance either of the sections below has the same effect as the first atomic section example listed above amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 O 1 55 amp amp atomic atom vdw2 mass H1 1 20 2 00 H2 1 20 2 00 O 1 55 amp Atoms may be described in more than one set of atomic input values but the same keyword cannot be used more than once for the same atom For example the following syntax is supported amp atomic atom basis C1 6 31g atom formal C11 amp but the following syntax is not supported amp atomic atom basis C1 6 31g atom basis C1 cc pVTZ amp Jaguar 6 0 User Manual 227 Chapter 9 The Jaguar Input File 228 To print an atomic section in the restart file that contains information for all atoms not just some set the output keyword ip29 to 2 If an atomic section exists or if ip29 2 in the input file the atomic section is echoed in the output from the program pre 9 8 2 Keywords That Specify Physical Properties The keywords that specify physical properties of atoms are listed and defined in Table 9 42 Values for these keywords can appear in restart files Table 9 42 Keywords for physical properties in the atomic section Keyword Description isotope Isotopic number integer e g 2 for deuterium overridden by atom s mass setting if it exists mass
480. should contain a line for each atom pair describing atoms to be treated at the LMP2 level Each line describing an LMP2 pair should begin with two atom numbers or labels which specify the two atoms in the pair Pairs can be listed in any order The following Imp2 section requests treatment of atoms 6 9 and 10 in the zmat section at the LMP level and all other atoms at the Hartree Fock level Atom 9 is bonded to atoms 6 and 10 amp lmp2 6 9 9 10 amp You can also use the Imp2 section of the Jaguar input file to list particular LMP2 pairs and request that they be delocalized over listed atoms With LMP2 delocalization the space of correlating virtual orbitals for an LMP2 occupied orbital is extended to include orbitals on nearby atoms To delocalize a bond pair on two particular atoms over a space including orbitals on a set of other atoms add a line to the Imp2 section listing the atom labels or numbers of the two atoms upon which the bond pair is located by default followed by the atom numbers or labels of the atoms over which the pair is to be delocalized Next set the keyword idelocv in the gen section to 1 to treat all LMP2 pairs in the system or 2 to perform a local local MP2 calculation with only the pairs listed in the Imp2 section treated at the LMP2 level For example the following gen and Imp2 sections request a local local MP2 calculation with the C2 C3 bond pair delocalized over C1 and C4 as well as over C2 and C3
481. sing Function File When Jaguar fits a function s grid point values to a basis set to find the applicable basis set coefficients for the function it uses dealiasing functions to reduce errors The dealiasing func tions span the function space determined by the grid more completely than the basis functions so a function on the grid can be better described using the dealiasing functions than by the basis functions alone The basis set coefficients for the function can then be determined by using the overlap between the dealiasing functions and the basis set functions which is deter mined analytically Some basis functions die off slowly and require long range functions centered on each atom in the molecule while others die off quickly over distance and can be described with short range dealiasing functions centered on the nearby atoms The latter type can employ different dealiasing functions depending on the distance between the atom upon which the relevant basis function is centered and the atom upon which the short range dealiasing functions are to be centered If the atoms are the same home atom dealiasing functions are used otherwise the distance between the two atoms determines whether the dealiasing functions used should Jaguar 6 0 User Manual 249 Chapter 10 Other Jaguar Files 250 be those for first order or one of the other higher order neighbors If the two atoms are further away than the farthest neighbor range
482. sis If nboden 0 or is not set at all the HF density is used NBO calculations require an SCF calculation to be performed first For more details on NBO input and output see the NBO 5 0 Manual or visit the NBO web site http www chem wisc edu nbo5 Jaguar 6 0 User Manual Chapter 10 Other Jaguar Files Jaguar needs certain types of files in order to run a job An input file must be created of course but additional files specifying the basis functions data for the initial guesses dealiasing func tions grids and cutoffs used during a run are generally necessary as well Unless other files are specified in the input data Jaguar uses the files default basis default atomig default daf default grid and default cutoff which are in the data directory For many solvation calculations Jaguar also uses the file de ault lewis All of these files are provided in the Schr dinger product distribution If you want to use other data files than those described above you can create a new data direc tory and put files in it whose names and formats match those described above When you run a job you can edit the input file and add BASISFILE ATOMIGFILE DAFFILE GRIDFILE CUTOFFFILE or LEWISFILE lines with the paths and names of the files you want to use See Section 9 1 on page 167 for more details You should avoid naming a cutoff file accurate cutoff quick cutoff or solvent cutoff because the program assumes you are using an out
483. sity W Molecular orbitals Alpha From HOMO Beta 0 From HOMO u 0 Total number of orbitals 2 to LUMO 0 to LUMO fo Total number of orbitals 2 start Read Write Edit Reset Close Help Figure 4 11 The Properties folder showing controls for surfaces You can view multiple surfaces for the same molecule but they are superimposed If you want to view multiple surfaces e g plots for several orbitals from the same molecule side by side you must duplicate the Project Table entry for the molecule as many times as you have orbitals to view then display a separate orbital surface for each entry In addition to displaying isosurfaces for the data generated by Jaguar you can display the value of the property for which you generated the data as a color map on another surface that is generated by Maestro For example you can display the value of the electrostatic potential on the van der Waals surface generated by Maestro To do this select the surface that you want to map the data to in the Surface Table panel and click Display Options In the Display Options dialog box select Map values from volume data and choose a volume from the list below Jaguar 6 0 User Manual 85 Chapter 4 Options 86 rface Table CC enzene dft 01 WILHELM I Area S benzene dft Ol benzene orb MO 20 E 0 209055 Demo oe LEE UE IEEE 24 898 benzene_orb MO 22 E
484. son Boltzmann equations 71 Poisson Boltzmann solver 71 73 output from 121 polar PIOSTAN anna 240 polarizability analytic t naio ee Eai eE Eit 77 keywords 196 198 Maestro options essen TT post progran i a ae etn 240 output TOU a crt ter trenes 121 potential energy surface scan 98 102 potential electrostatic output on Eid rennen 198 ure 84 Powell update method keyword 189 pre programa ocsocsedieomen e se 239 output from 110 118 120 Preferences panel sess 25 26 pressure for thermochemical calculations keyword option oiii P RFO level shifting keyword for probe pfogrfam naneseneie a 239 probe radius of solvent 73 340 processors determining optimum number 306 selecting number of 276 setting number available on a host 272 product geometry for IRC calculations 104 in transition state search 94 specifying in input file 171 specifying in Maestro sees 95 product installation eee 333 program order specifying 239 241 programs in Jaguar see relevant program name project CHUTES nennen 12 Project Facility introduction
485. specified no dealiasing functions on one atom are used in calculating the contribution of a short range basis function centered on the other atom The dealiasing functions themselves are simple polynomials multiplied by Gaussian functions and are s type p type and so on depending on the polynomial Uncontracted dealiasing func tions are simply formed by specifying the exponent of the Gaussian function Contracted dealiasing functions are defined as linear combinations of the appropriate type of functions the coefficients and exponents for the linear combination are the same as those used in the basis set for the contracted basis functions for the relevant function types 1s 2s 2p etc depending on the molecule and the basis set Thus a dealiasing uncontracted function can be specified by dictating the type s p d etc and the exponent desired for the Gaussian while a contracted Gaussian function can be specified by dictating the type and referencing which set of contrac tion coefficients and exponents are desired Section 10 3 1 below describes the file that determines the dealiasing functions for a calcula tion Sets of dealiasing functions must be provided for each grid used in the calculation Comments about a sample file refer to the sample da file in Section 10 3 2 on page 252 10 3 1 File Format and Description The first line of a dealiasing function file contains a character string which includes the version number of Ja
486. spectral method to be maintained for GVB calculations The method yields very accurate excitation energies rotational barriers and bond energies for many mole cules and GVB calculations with Jaguar are typically 10 to 100 times more efficient than the best conventional GVB programs even for molecules as small as ten atoms 6 In the GVB approach each bond or other electron pair is described by two non orthogonal orbitals whose contributions to the bond description are obtained variationally The bond description can thus change smoothly from a description with two atomic like orbitals at large bond distances to a description with bond like orbitals at short distances This improvement over Hartree Fock which treats bonds as having equal amounts of covalent and ionic char acter allows GVB to describe charge transfer reactions and bond breaking and formation accu rately and also gives better results for other molecular properties than an HF treatment alone can provide Jaguar 6 0 User Manual 157 Chapter 8 Theory 158 The goal of a GVB calculation then is to obtain pairs of GVB orbitals y and y where p ranges from 1 to the number of GVB pairs N that lead to a minimum energy for the molec gvb ular wave function N ovb Y II V 54V po V ppV pa CB Boo 4 p l For a given p the orbitals y and Y form a pair that describes a particular bond or other pair of electrons Under the perfect pairing restrict
487. st explicitly set irder 1 and the derivatives must be calculated numerically by setting nmder 2 The calculation of IR intensities involves the calculation of the dipole moment derivatives If you only want to calculate dipole moment derivatives using the Hartree Fock method but don t want to do the frequency calculation that is normally required to get them you must set up a special path section see Section 9 16 on page 239 with the appropriate sequence of executa bles to run The path section to use is amp path pre onee hfig probe grid rwr scf ira rwr irb amp You must also set irder 1 isymm 0 and ifreq 1 The ifreq setting is necessary to force tight accuracy in the SCF but no frequency calculation is actually performed To compute partial frequencies for a fragment you must first define the fragments in the atomic section then make the setting fregfrag fragno in the gen section of the input file for the frequency calculation These settings are in addition to any other frequency related settings 9 5 15 Basis Set Keywords The character string keyword basis allows you to override the default basis set 6 31G This keyword should be a string describing the standard basis and any desired polarization and diffuse functions The string describing the standard basis should be chosen from the first Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File column of Table 4 1 on page 56 or Table 4 2 on page 58 Lowercase or u
488. sults to refine the initial Hessian to be used for the opti mization To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the variable definition section For instance either of the following two input geometries will have the same effect a job that includes Hessian refinement will use both O H bonds and the H O H angle in the refinement O1 H2 O1 se H3 O1 qu dos H2 108 0 or O1 H2 O1 ohbond H3 O1 ohbond H2 108 0 ohbond 1 1 Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refine ment For example for the second water example shown above only two coordinates are actu ally refined the O H bond distance which is the same for both bonds and the H O H angle The same would be true for the first example if molecular symmetry were used for the job 3 5 Reading Files If you already have Jaguar input files containing geometries either with or without informa tion on the type of calculation to perform you can read them using the Jaguar Read dialog box which you open by clicking the Read button in the Jaguar panel This dialog box is a file selector with the usual file browsing tools a Filter text box a Directories list a Files list and a Selection text box By default information is displayed for the current workin
489. t 114 143 density functional theory DFT 59 63 164 165 hybrid methods sss 60 63 key WOAS caeteros ttes output from standard functionals density matrix convergence Criterion convergence criterion keyword in DIIS error vector keyword for output density see electron density spin density derla program 240 Output from nri 117 120 derlb program eerte 240 Output OM seiis seiate 117 120 derivatives of basis functions 138 keyword for list in output 213 dftname values name strings for construction of 181 standard functional names 180 DFT see density functional theory dielectric constant keyWotds iiecesete crier retire tentes 195 keywords for crisissen mensi 195 setting in the Solvation folder T3 dielectric continuum method see pb program DIIS convergence scheme 70 113 143 keyword for coefficient output 216 key Words eoe imer 201 202 Output een 114 dipole moment see multipole moments Direct Inversion in the Iterative Subspace meth od see DIIS convergence scheme directory current working eene 4 25 executable ES input 287 install tion i2 u 0s ike ideato 269 OULPUE eee eee eeee eee 25 283 287 schrodinger hosts
490. t containing very floppy molecules transition metal complexes poor initial geometries or poor initial Hessians may require many more cycles and in particularly bad cases may also require you to stop the calculation and restart it with a change in one or more of the other default settings described below 5 1 2 The Initial Hessian To perform an optimization Jaguar first needs to read or generate an initial Hessian second derivative matrix or force constant matrix The Hessian and the gradient are used to define a search direction that should result in a lowering of the energy You can provide Jaguar with a Hessian in the hess section of an input file as described in Section 9 9 on page 234 For instance if you restart a geometry optimization from a previous job as described in Section 7 5 on page 150 Jaguar automatically uses the Hessian provided in your input file If you want to provide an initial Hessian in the input file choose Other from the Initial Hessian option menu If your input file does not contain a Hessian you can use the Initial Hessian option menu in the Optimization folder to specify what kind of initial Hessian Jaguar should generate You can select from among several internal guesses the Fischer Alml f Hessian 53 the Schlegel Keyword dconv in the gen section Keyword iaccg 2 in the gen section Keyword iaccg 3 in the gen section Keyword maxitg in the gen section Keyword inhess 2 in the gen section
491. t incorporated you can read the restart file into the Jaguar panel then import the vibrational data by choosing Import Vibrational Data from the Selection menu in the Project Table panel To view vibrational animations from calculations run with previous versions of Jaguar you can quickly generate the vib file using the Jaguar restart file from a frequency calculation using the following procedure 1 Read the restart file into the Jaguar panel The structure is displayed in the Workspace and an entry is created in the Project Table 2 Choose Initial Guess Only from the Jaguar submenu of the Applications menu 3 In the Properties folder select Vibrational frequencies in the table then select Use avail able Hessian in the Vibrational frequencies section 4 Run the job Vibration vibration Entry trans state inci Choose Frequency 2031 212 0 571 192014 623 569683 765 362144 Animate Amplitude 1 000000 Slower Faster Speed EL 7 a ex Figure 4 10 The Vibration panel Jaguar 6 0 User Manual Chapter 4 Options An alternative to steps 2 and 3 is to edit the input file and in the gen section change ifreq 1 to ifreq 1 and add igonly 1 The former setting means use available Hessian for calculating frequencies and the latter setting means skip the SCF The job should take only a few seconds even for a large molecule When the job finishes a new entry is added to the
492. t the calculation with the wave function and other data already calculated you can just read in the new input file The file name is jobname in where the asterisks represent a two digit number This number is 01 if the name of the input file for the job from which it was generated is not in this form and is otherwise set to the number after that assigned to the current input file These files overwrite any other existing files of the same name Jaguar 6 0 User Manual Chapter 7 Using Jaguar As an example if you run the job h2o the restart file generated during the run is called h20 01 in You could then read this file as described in Section 3 5 on page 41 and use it to continue on with the calculation possibly after making some changes to the calculation requested The new input file generated during this second run would be called h20 02 in If you want to start a new job where the previous job left off you need only read the new input file in then make any changes you think are necessary for example you could change the SCF energy convergence criterion in the SCF folder Similarly if you want to perform an addi tional calculation once a geometry has been optimized you can read in the restart file as input for the second job and make any necessary changes to it such as selecting a GVB calculation instead of Hartree Fock Section 3 5 on page 41 contains information on reading input files in the GUI See Chapter 9 if you wo
493. te the next element s bonding types are about to be described in the same format After all desired bonding types are described for all appropriate elements the bonding type information should end with a blank line 10 6 2 Describing Hybridization Types in the Lewis File The hybridization type information in the Lewis file includes up to five groups for each element described where each group indicates a set of elements and hybridizations for those elements The hybridization applies to the atom to which the original element is bonded The information for hydrogen s first group for instance could list C atomic number 6 with sp hybridization allowing a later line in the Lewis file to set a particular radius for hydrogen atoms bonded to sp carbons The format of the hybridization type information is very similar to that of the bonding type information The first line of this information for HF GVB or DFT calculations should begin HYBRIDIZATION TYPE 01 and the rest of the hybridization type information should not contain any blank lines except the last line which signals the end of hybridization type information Hybridization type information should be listed for each relevant element in turn The informa tion for the first atom should follow immediately after the HYBRIDIZATION TYPE 01 label The first character of the information for that atom should begin with the atom s atomic number The following lines should describe up to
494. tera tions The cutoff sets themselves are provided later in the file and dictate the level of analytic corrections the grid and the non default values of the gen section cutoff keywords cutl for example The cutoff sets are described in more detail below The columns reflect a scheme in which calculations are broken down into preliminary and final sets of iterations The iterations from the beginning of the first SCF calculation in a run are considered to be part of the prelim inary set while the iterations from the end of the first SCF calculation or from any subsequent set of SCF iterations are considered to be part of the final set For instance for a solvation calculation the SCF iterations for the analysis of the converged gas phase wave function are preliminary iterations followed by final iterations while the SCF iterations for all subsequent SCF calculations those including the solvent effects are final iterations Jaguar determines how many iterations are preliminary and how many are final for the initial SCF calculation The number in the first column in each of the five accuracy level lines dictates the cutoff set used for the first iteration in the preliminary sequence if the number is a 1 the first cutoff set listed in the file is used if it is a 5 the fifth is used and so on The number in the second column provides the cutoff set used for updates during the preliminary sequence of iterations The third and fourth columns
495. tes to run both sites protonated one site protonated two cases and no sites protonated If one obtains data for these four cases the titration curve can be assembled and one can make comparison with experiment Cases 1 and 2 are straightforward to handle When the ionizable groups are close together in the molecule the calculated pK may not be as accurate because the two groups could interact in ways that the existing parameterization cannot handle For case 3 you must run two separate pK jobs each of which handles two of the four protonation states and build the titration curve by hand 14 3 Training Set Results Table 14 1 presents a summary of the results for the functional groups for which parameters are available including the number of cases studied average deviation from experiment and maximum deviation The functional groups are classified as acids and bases for bases it is the pK of the conjugate acid that is computed A listing of the results for the individual test cases comparing experimental and calculated pK values can be found in Table 14 2 The largest set of test cases examined have been for carboxylic acids and nitrogen bases in heterocyclic rings The latter cases have minimal conformational flexibility and hence should be easier to handle and this is indeed reflected in the remarkably low average error of 0 2 and maximum error of 0 4 that we observe The carboxylic acids include some examples with polyf
496. th a field of E in the x direction and four others with fields of E and E in the y and z directions The 5 point method uses the same data as the 3 point method as well as data from SCF calcula tions using fields of aE and aE in the x y and z directions where a is some constant Simi larly the 7 point method uses the same data as the 3 point method plus data obtained using fields of aE aE bE and bE in the x y and z directions where a and b are some constants By default the magnitude of the electric field E is 0 024 au If you want to use a different value set the efield keyword to the desired value AII polarizability methods are run with symmetry off that is the keyword isymm is set to 0 automatically if ipolar 0 Similarly for any polarizability calculation the keyword econv which gives the energy convergence criterion is set by default to 1 0x10 although if the calculation first satisfies the criterion dictated by the keyword dconv the energy convergence criterion is ignored When charge fitting is constrained to reproduce multipole moments that is when incdip 0 the keyword cfiterr determines whether the multipole moment constraint is too restrictive to produce adequate charges if the error in the total resultant charges is more than cfiterr the charge fitting is rerun with a lower multipole moment constraint The keyword wispe is used to set the spacing of the rectangular grid for electrostatic potent
497. the Display menu 2 In the Composition folder select Element and Atom Number 3 In the picking tools section at the top of the panel you could do one of the following Click Selection to apply labels to the atoms already selected in the Workspace from the previous example Choose Residues from the Pick option menu and click on an atom in a different res idue to label all the atoms in that residue 2 6 3 The Atom Selection Dialog Box If you wish to select atoms based on more complex criteria you can use the Atom Selection dialog box To open this dialog box choose Select from a button menu or click the Select button in a panel See Section 4 3 of the Maestro User Manual for detailed instructions on how to use the Atom Selection dialog box 2 7 Scripting in Maestro Although you can perform nearly all Maestro supported operations through menus and panels you can also perform operations using Maestro commands or compilations of these commands called scripts Scripts can be used to automate lengthy procedures or repetitive tasks and can be created in several ways These are summarized below 2 7 1 Python Scripts Python is a full featured scripting language that has been embedded in Maestro to extend scripting facilities The Python capabilities within Maestro include access to Maestro function ality for dealing with chemical structures projects and Maestro files The two main Python commands used in Maestro are python
498. the OCBSE convergence scheme is selected the Coulomb and exchange contributions to the total two electron terms are listed in the SCF summary below the table If a fully analytic calculation is performed see Section 4 2 on page 55 the programs grid and rwr are not run because the all analytic method does not use this code If you select a Final localization method the output from the program local appears after the output from any SCF iterations and lists the orbitals that are localized If you want to print out the localized orbitals you should make the appropriate selection in the Output folder as described in Section 6 6 on page 139 6 4 Options for Extra Output The options available in the Output folder of the Jaguar panel under Extra detail to be written to output file are described in this section These options are presented as a list from which you can select multiple items with the SHIFT and CTRL keys The output generated from these options appears in the output file for the job If you make a non default setting the output from the program pre prints the non default options chosen This output appears above the molecular geometry output from pre and gives the non default values of the keywords referred to in footnotes throughout this section Echo input file and parameter list If you turn this output option on the output from the program pre includes an echo of the input file a description of the path which indicates
499. the molecule in the gas phase are calculated The program ch performs electrostatic potential fitting which represents the wave function as a set of point charges on the atomic centers The interactions between the molecule and the solvent are evaluated by Jaguar s Poisson Boltz mann solver which fits the field produced by the solvent dielectric continuum to another set of point charges These charges are passed back to sc which performs a new calculation of the wave function for the molecule in the field produced by the solvent point charges Electrostatic potential fitting is performed on the new wave function the solvent molecule interactions are reevaluated by the Poisson Boltzmann solver and so on until the solvation energy for the molecule converges For solvation calculations on neutrally charged systems in water whose atoms all have atomic numbers under 19 H Ar by default the program pre evaluates the Lewis dot structure for the molecule or system and assigns atomic van der Waals radii accordingly For more information on this process see Section 10 6 on page 260 These van der Waals radii are used to form the boundary between the solvent dielectric continuum and the solute molecule The Lewis dot structure and van der Waals radii information both appear in the output from the program pre The radii are listed under the heading vdw2 in the table of atomic information below the listing of non default options See Section 9 8 on p
500. the outermost core orbitals e g 5s5p6s5d6p for W The last letter in each LA basis set name refers to the basis set used for atoms not described by ECPs S indicates the STO 3G basis set D indicates the D95V basis set and P indicates the 6 31G set developed by Pople and coworkers Note that in addition for some atoms the LACVD and LACVP basis sets use the same basis functions as the LAV3D and LAV3P basis sets respectively The Los Alamos effective core potentials which were developed by Hay and Wadt include one electron mass velocity and Darwin relativistic corrections for elements beyond Kr Jaguar 6 0 User Manual 57 Chapter 4 Options 58 Table 4 2 Basis sets contained in Jaguar that include effective core potentials Basis Set Atoms in ECP Other Atoms Options Refs LAVIS Na La Hf Bi H Ne STO 3G H Ne 97 98 LAV2D Na La Hf Bi H Li Ne D95V H Li Ne 97 98 LAV2P Na La Hf Bi H Ne 6 31G H Ne 97 98 H Ne LAV3D Na La Hf Bi H Li Ne D95V H Li Ne 97 98 LAV3P Na La Hf Bi H Ne 6 31G c H Ne 97 98 H Ne LACVD K Cu Rb Ag H Li Ne D95V Na Ar H Li Ne 99 Cs La Hf Au Zn Kr Cd Xe Hg Bi LAV3D LACVP K Cu Rb Ag H Ar 6 31G Zn Kr Cd H Ar 99 Cs La Hf Au Xe Hg Bi LAV3P H Ar LACV3P K Cu Rb Ag H Ar 6 311G Zn Kr H Ar 100 Cs La Hf Au Cd Xe Hg Bi LAV3P H Ar plus metal dif fuse d CSDZ Ce Lu H Ar 6 31G Zn
501. the pruning scheme and the distribution of the radial shells The keywords and their settings have the form ndfgrdX1 nr ndfgrdX2 na idfgrdX pqq gt 66 66 where X is m f g u d or c signifying medium fine gradient ultrafine second derivatives and CPHF and correspond to grids 10 11 12 13 8 and 9 nr is the number of radial shells na is the angular grid entry number from Table 10 1 p is a number denoting the radial shell distribution scheme and qq is a two digit number denoting the pruning scheme The possible values for p are 1 geometric distribution 145 the default for medium fine and gradient grids 2 Becke s Gauss Chebyshev distribution 146 3 described in ref 147 and 4 the Mura Knowles distribution 148 the default for the ultrafine second derivative CPHF and grid 14 The values of qq can be 00 11 22 or 33 00 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File is the default for the medium grid 11 is the default for the fine and gradient grids and 33 is the default for the second derivative CPHF and ultrafine grids 22 turns off pruning The value for ndfgrdX2 is interpreted as an offset to be added to the angular value for each radial shell that is determined from the pruning scheme You can get more information about both pseudospectral and DFT grids for a job by setting ip23 2 in the input file Table 9 37 show
502. the usual fashion 1 Do density averaging before DIIS starts mixing in some of old orbitals with new orbitals default for DFT calculations lastwv 0 Skip diagonalization of Fock matrix on last iteration 1 Diagonalize Fock matrix on last iteration nosuper 0 Evaluate integrals simultaneously over s and p basis functions with the same exponents superblocks 1 Evaluate integrals separately for s and p basis functions which have the same exponents 2 Use superblocks for all integrals except for gradient itwice 1 Do A integrals once in SCF routine 2 Do A integrals twice in SCF routine required for GVB optional for HF ichange z Change all cutoffs except those related to S eigenvalues bc pairs or ab distance cutoff for exchange by a factor of 10 to the ichange power dconv 5x10 SCF density convergence threshold RMS change in density matrix econv 5x10 SCF energy convergence threshold in hartrees maximum difference in energy between one SCF iteration and the next required for convergence Default is 1e 6 for polarizability and hyperpolarizability stdiis 100 0 DIIS initiation threshold DIIS is started when the largest value of the DIIS error vector is less than this value vshift 0 0 Level shift for virtual orbitals the amount the virtual orbital energies are increased before diagonalization in hartrees Default for pure DFT is 0 3 for hybrid DFT is 0 2 ifdtherm 0 Do not use thermal smearing in DFT or HF calculations 1 Use frac
503. they will continue to be supported You should use the new equivalents To run a Jaguar job you first need a Jaguar input file The file should be named in the form jobname in You can create an input file using the GUI see Section 3 3 on page 34 for more information If you create or edit an input file using a text editor make sure its format agrees with that described in Chapter 9 You can run a single Jaguar job from the command line with the command jaguar run jobname in 276 Jaguar 6 0 User Manual Chapter 11 Running Jobs where jobname is the stem of your input file name jobname in Jaguar supplies the in extension if you omit it With this command the job runs on the machine upon which you have submitted the command and uses the most recent version of Jaguar To run a Jaguar job on another machine use a command in this form jaguar run HOST hostname jobname where your input file is named jobname in and hostname is one of the hosts in the file schrodinger hosts For instance if you were logged into a machine named alpha and wanted to run a job named ch4 on a machine named beta you would enter jaguar run HOST beta ch4 To run a Jaguar job on the machine hostname with a particular non default set of executables you can use the command jaguar run HOST hostname VER version jobname where version is any string that appears in one of the executable directories listed for that host by the command jaguar
504. ths or angles of the geometry so that they are frozen during the optimization as described in Section 5 2 on page 90 the constraints are also listed in the pre output At the end of the first SCF calculation the programs der1a rwr and der1b run calculating the forces felt by each atom in the unoptimized geometry and writing them to the output file as described above These force results are followed by the output from the program geopt which includes a number indicating how many times it has been called in the start of program geopt line Every time geopt is called this number is updated However since geopt can be called for Hessian refinement steps as well as for generating new geometries during an optimization and since geometry optimizations occasionally revert back to a previous geometry and restart the calculation from there the next line of the geopt output reports what sort of step is being performed and numbers that step accordingly If the program detects that the input lists separate fragments each of which contain only atoms unbonded to the atoms in any other fragment as for a van der Waals complex then the number of fragments is listed near the start of the geopt output For transition state optimizations the eigenvalues of the nuclear Hessian are reported the first time geopt runs If the initial Hessian is being refined the coordinates for the refinement and their eigenvalues are listed If a coordinate you hav
505. tings start the job by clicking Start The Monitor panel opens and displays the Jaguar log file for the job As the job runs this file is updated If you close the Monitor panel the updating ceases You can reopen the panel later by choosing Monitor Jobs from the Applications menu To monitor the job again select it in the table and click Monitor See Section 2 10 on page 26 and Chapter 14 of the Maestro User Manual for more information on job control and monitoring Any additional jobs that you submit run concurrently If you exit Maestro any Jaguar jobs still running continue to run to completion 3 10 Running Jaguar Batch Jobs You can run multiple Jaguar calculations in a single run using Jaguar batch scripts Some of the kinds of calculations you can run with a batch script are Multiple independent jobs with predetermined input files The same type of job for several input geometries A series of jobs in which later jobs use files generated during earlier jobs Several Jaguar batch scripts are included with Jaguar You can also write your own batch scripts or save job settings as a batch script in the Jaguar Write dialog box Maestro writes temporary batch scripts and runs a batch job whenever you run jobs with multiple structures as input that do not have geometry dependent settings Section 11 3 on page 282 provides details on batch scripts Jaguar 6 0 User Manual 49 Chapter 3 Running Jaguar From Maestro 50 Ja
506. tion provides instructions for running a sample calculation on the water molecule The sample calculation runs only if Jaguar has been correctly installed If the calculation does not run try the suggestions in Chapter 12 or see your system manager or the person who installed Jaguar at your site Contact Schr dinger if you cannot resolve the installation problems First log on to a machine where the Maestro and Jaguar software is installed Change to the directory where you want the Jaguar output files for the sample job to be written then start Maestro by entering the command Jaguar 6 0 User Manual 29 Chapter 3 Running Jaguar From Maestro 30 SSCHRODINGER maestro amp If SSCHRODINGER is in your PATH environment variable you can simply type maestro Once Maestro is running choose Single Point Energy from the Jaguar submenu of the Applications menu to open the Jaguar panel for a single point energy calculation see Figure 3 1 on page 33 The next step is to enter a molecular geometry structure You can enter the structure by hand or read it from a file To enter the structure by hand you can use the Edit Job window Click the Edit button select the Structure option then click in the text area and type the following lines Oo 0 0 0 0 0 1135016 H1 0 753108 0 0 0 4540064 H2 0 753108 0 0 0 4540064 The labels begin with element symbols O and H The numerals 1 and 2 appended to the hydrogen labels distinguish betwe
507. tional occupation number FON method for thermal smearing 133 2 Use pseudo fractional occupation number pFON method for thermal smearing 133 204 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 28 Keywords for methods used in the SCF convergence procedures Continued Keyword Value Description fdtemp 10000 Initial temperature in K for thermal smearing icanorb 0 Allow number of canonical orbitals to vary during calculation 1 Fix number of canonical orbitals during calculation ncanorb gt 0 Number of canonical orbitals to keep during calculation Another method for controlling SCF convergence is thermal smearing 133 which improves convergence in difficult cases by using a fictitious temperature to fractionally occupy all orbitals occupied and virtual and then decrease the temperature until convergence is reached The orbital occupation numbers are represented by a Fermi Dirac function n 1 l exp 8 kT Two methods for determining the occupation numbers have been implemented FON fractional occupation number and pFON pseudo FON In the FON method the Fermi energy is determined so that the resulting occupations sum to the total number of electrons In the pFON method a Fermi energy is assigned halfway between the HOMO and LUMO energies and then the resulting occupations found from this Fermi energy are renormalized so that they sum to the total number of electrons Thermal smearing is turned on
508. tions much like any other table select rows by clicking shift clicking and control clicking However because clicking in an editable cell of a selected row enters edit mode you should click in the Row column to select entries See Section 2 4 5 on page 16 for more information on mouse actions in the Project Table There are shortcuts for selecting classes of entries on the Select menu In addition to selecting entries manually you can select entries that meet a combination of conditions on their properties Such combinations of conditions are called filters Filters are Entry Selection Language ESL expressions and are evaluated at the time they are applied For example if you want to set up a Glide job that uses ligands with a low molecular weight say less than 300 and that has certain QikProp properties you can set up a filter and use it to select entries for the job If you save the filter you can use it again on a different set of ligands that meet the same selection criteria To create a filter 1 Do one of the following Choose Only Add or Deselect from the Select menu Click the Entry selection button on the toolbar X 2 In the Properties folder select a property from the property list then select a condition 3 Combine this selection with the current filter by clicking Add Subtract or Intersect These buttons perform the Boolean operations OR AND NOT and AND on the corre sponding ESL expressions 4 To
509. to set GVB pairs automatically The appropriate keywords are listed in Table 9 6 The Lewis dot structure code finds several alternative Lewis dot structures for resonant mole cules assigning bonds as single double or triple bonds unambiguously For instance it finds two structures for benzene depending on the assignment of the pi bonds For these cases you might want to run Jaguar with lewdot 1 and lewstr 0 which will cause it to print out all Lewis dot structures it finds then exit At that point you can figure out which structure you want to use to set the GVB pairs set lewstr igvball and igvbsel accordingly and set lewdot 1 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File If you know there is only one reasonable Lewis dot structure for the molecule you can set igvball and igvbsel At that point lewdot and lewstr are set to 1 by default The values for igvbsel are easier to remember if you associate the number 1 with sigma pairs 2 with pi pairs and 4 with GVB lone pairs Then to print out any combination of these pair types you set igvbsel to equal the sum of the numbers associated with the pair types you want to print Table 9 6 Keywords for evaluation of Lewis dot structures and application of that information to GVB pair settings Keyword Value Description lewdot 0 Do not find Lewis dot structure s or use them to set GVB pairs Find Lewis dot structure s and continue on with ca
510. tom 6 with one bond from carbon s Group 2 a double bond to either C or O and two bonds from carbon s Group 1 single bonds to H and would set such an atom s radius to 2 00 unless another matching description preceded that line The rightmost digit in the integer describing bonding type specifies the number of bonds formed by the atom which are not of any of the forms described in the groups for that atom s bonding type information A double or triple bond counts as one bond not two or three and lone pairs should not be included in the bond count The digits of the bonding type integer must describe all of an atom s bonding in order to match the atom information For example if the Lewis file described above contained no group for C C bonds in the bonding type information the integer 200 would only describe a carbon atom with one double bond to another C or O and no other bonds while the integer 202 would adequately describe a carbon with one double bond to another carbon and two single bonds to other carbon atoms The fourth integer in an atom type description which describes hybridization type or the elements and hybridization of the atoms to which an atom is bound works almost the same way as the integer describing bonding type As it does for bonding types the digit g places from the rightmost digit in the integer represents the gth group in the hybridization type infor mation for that element see Section 10 6 2 on p
511. tom has A bonding type group describes elements of bonded atoms and orders of those bonds as described in Section 10 6 1 The third integer in an atom type description line determines how many bonds the atom forms of each bonding type group g for an atom of a particular element where g indicates the order of the bonding type groups listed for that element The number of bonds from group g is indicated by the 10 digit in the integer For example if g were 1 and the atom being described were carbon g would correspond to the first bonding type group listed for carbon and a bonding type integer value of 40 4 x 10 would indicate that that carbon atom had four bonds from carbon s Group 1 bonding type Jaguar 6 0 User Manual 265 Chapter 10 Other Jaguar Files 266 information If the Lewis file contained the bonding type information example provided in Section 10 6 1 which included the lines 6 CARBON Group 1 C H bonds only Group must be here the rest is a comment Bond order 1 this should be a non blank comment line 1 element 1 the atomic number of H the integer value of 40 would describe a methane carbon The same sample Lewis file informa tion whose key Group 2 information for carbon appears in these lines Group 2 C C and C O bonds Bond order 1 0 elements Bond order 2 2 elements 6 8 would mean that this radius information line 6 1 120 1 1 1 2 00 C in H2 C C or H2 C O would describe a carbon a
512. traint If you edit the input file to add constraints you can freeze a specific coordinate by adding a sign at the end of its value in your geometry input in either the zmat or the zvar section For example to fix the HOH bond angle of water at 106 0 you could use the following Z matrix Oo H1 O 0 9428 H2 O 0 9428 H1 106 0 If you performed a geometry optimization on this input geometry the bond angle would remain frozen at 106 while the bond lengths varied To freeze a variable during an optimization add a sign to the end of the variable setting In this example the C H bond is frozen at 1 09 A chbond 1 094 HCHang 109 47 You can also freeze a variable by adding a sign to the variable in the Z matrix or the Carte sian coordinate list For example in the following input for optimization of a water molecule the H atoms are only allowed to move within the xy plane in which they started Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoori H2 0 000000 ycoor zcoori ycoorz0 753108 zcoorz0 454006 Jaguar 6 0 User Manual 91 Chapter 5 Optimizations and Scans 92 If frozen Cartesian coordinates are included in the input for an optimization Jaguar uses Carte sian coordinates for the optimization rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry 5 2 2 Applying Constraints by Using Variables When you define a set of c
513. trix elements V5 i far er xclP a cry e N Guy 23 where f p Vp is an exchange correlation functional and y is J Vp Vp The exchange correlation functional f p Vp is usually separated into exchange and corre lation functional components that are local or non local in the density fp VP Flpl f wrle Vel Klpl f wp Vol 24 Under the local density approximation LDA the non local functionals f nz p Vpl and Je n lp Vpl are ignored when either or both of these terms are included the generalized Jaguar 6 0 User Manual Chapter 8 Theory gradient approximation GGA also known as the non local density approximation NLDA applies The local and non local exchange and correlation functionals available within Jaguar are described in Section 4 3 on page 59 and its references The electronic ground state energy E is given by loo 1 Ey 2y jawey V Jer V uT pE deo Jer f p Vpl 25 in Hartree atomic units where V is the nuclear potential and J is the Coulomb potential Therefore for a given exchange correlation functional it is possible to solve iteratively for Kohn Sham orbitals y r and the resulting density p to yield a final DFT energy A more detailed description of density functional theory can be found in Refs 118 and 119 Jaguar 6 0 User Manual 165 Chapter 8 Theory 166 Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File This chapter describes the Ja
514. ts the available basis sets in Jaguar that do not use effective core potentials The table indicates the atoms these basis sets can describe and shows which sets include the options of polarization and diffuse functions The cc pVDZ and cc pVTZ basis sets include polariza tion functions by definition Table 4 1 also indicates the method used for the calculation the fast pseudospectral method or the slower analytic method in which four center two electron integrals are computed explic itly The analytic method is used only when optimized pseudospectral grids and dealiasing function sets for one or more atoms in the molecule are not available For molecules whose atoms are all in the range H Ar in the periodic table we recommend using the 6 31G basis set the default choice which is one basis set that permits pseudospectral calculations The column headed of d fns indicates whether d shells include the five real spherical func tions d dyz dyz d y2 and dy 2_ 2_ 2 all with the same angular momentum 2 or whether d shells include the six Cartesian d functions d 2 d 2 d dyy dyz and d This 4 Keyword basis in the gen section Jaguar 6 0 User Manual 55 Chapter 4 Options 56 choice also affects the dimension of the Fock matrix for diagonalization To override this selec tion select the Number of D functions option that corresponds to your preference or set the keyword numd in the gen section of the inp
515. u can use in the gen section of the input file to specify the functional The names are case insen sitive 4 4 Hartree Fock and CIS Settings In addition to selecting unrestricted UHF or spin restricted ROHF treatment of open shell molecules the controls available when you choose HF Hartree Fock from the Level of theory option menu allow you to set up configuration interaction singles CIS calculations for excited states These calculations are only available for a closed shell Hartree Fock reference wave function To do a CIS calculation select Excited state CIS You can then enter the number of states you want to generate in the Number of excited states text box and set a limit on the number of iterations in the diagonalization procedure in the Maximum CIS iterations text box 4 5 Local MP2 Settings The LMP2 Local MP2 option of the Level of theory option menu allows you to set up a local Mealler Plesset second order perturbation theory 45 48 calculation The local MP2 LMP2 method greatly reduces the basis set superposition errors that can arise from the canonical MP2 method 48 The LMP2 method is much faster than canonical MP2 and typically recovers 98 of the canonical MP2 energy correction The pseudospectral implementation of LMP2 is described in Section 8 3 on page 161 For closed shell systems you can perform LMP2 geometry optimizations charge fitting solvation calculations and many other options available
516. uar Command not found you can add the installation directory to your path as follows csh tcsh setenv PATH installation directory PATH bash ksh export path installation directory path Jaguar 6 0 User Manual Chapter 12 Troubleshooting 12 1 3 Problems Starting Maestro If you have problems when you try to start Maestro they are likely to involve permissions needed to do things over a network Most of these problems never arise if the machines you are using are within a local network If you are using only local hosts and still have these prob lems you might ask your system manager for advice in addition to following the instructions given here If you get the message Error Can t Open display you are probably trying to start Maestro from a machine that is not acting as your X server and this machine does not know what your display is Before starting Maestro you can specify the display with the following command substituting the name of your X server or terminal for displayhost csh tcsh setenv DISPLAY displayhost 0 0 sh bash ksh export DISPLAY displayhost 0 0 The error message Xlib connection to displayhost 0 0 refused by server Xlib Client is not authorized to connect to Server Error Can t Open display usually means one of two things First if you are not the person who initially logged on to the X server you cannot bring up any type of X window on the display In this case you should log
517. uares fitting matrix Q Keyword Value Description iqufine 0 For ultrafine grid compute Q on the fly in the program scf 1 For ultrafine grid compute Q in the program rwr and store on disk for later use iqgrad 0 For gradient grid compute Q on the fly in the program scf 1 For gradient grid compute Q in the program rwr and store on disk for later use iqlmp2 0 For LMP2 grid compute Q on the fly in the program sc 1 For LMP2 grid compute Q in the program rwr and store on disk for later use iglmp2grad 0 For LMP2 gradient grid compute Q on the fly in the program scf 1 For LMP2 gradient grid compute Q in the program rwr and store on disk for later use 9 5 26 Plotting Keywords You can generate a plot file using keywords in the gen section that contains the values of the density the spin density the electrostatic potential or orbital amplitudes The data values are tabulated on a rectangular grid the box which is generated automatically and encompasses the van der Waals radii of all atoms in the molecule The plot file can be used by Maestro and other programs to display surfaces for a particular value of the density potential or amplitude The length units for the grid are set with the iunit keyword The possible values of the plotting keywords are given in Table 9 41 See Section 4 12 on page 84 for information on setting up plot data using the GUI Orbital amplitude data can only be generated for SCF and
518. uesses but those for other calculations do not If SCF itera tions are performed the initial guess for the gau file is obtained from the resulting wave func tion otherwise it is generated from the appropriate Jaguar initial guess routine When Jaguar 6 0 User Manual Chapter 9 The Jaguar Input File Table 9 33 Effect of setting output keywords for files to 2 Keyword Description of What Is Printed When ipi 2 ip90 Molden orbitals file mo1f file ip160 GAUSSIAN 92 input file gau file see text for ip160 3 4 or 5 ip163 GAUSSIAN 92 basis set gbs file ip164 MOM basis set bas file ip165 SPARTAN 4 0 archive file appears in temp directory as spart arc to write arc file to local job directory instead use ip165 3 ip168 GAMESS input file gamess file ip172 RESP Restrained Electrostatic Potential 134 file resp file Set to 3 to include grid weights ip175 XMol file xyz file with geometries generated during optimization ip177 AIMPAC w n file which works with RHF ROHF but not UHF a See text in this subsection for information on ip151 and on other options for ip160 ip160 5 the basis set is included explicitly in the gau file rather than just the basis set name When ip160 4 the trial wave function and the basis set are included The format of the resp file created with the ip172 keyword is as follows The first line contains the number of atoms and the number of grid points at whic
519. ulation see the troubleshooting information in Chapter 12 Chapters 4 and 5 describe the available calculation options which allow you to specify which properties you want the program to calculate and which methods you want it to use Chapter 4 includes information on using generalized valence bond GVB restricted configuration inter action RCI Mgller Plesset second order perturbation theory and density functional theory DFT techniques calculating solvation energies vibrational frequencies hyperpolarizabili ties multipole moments and other properties fitting charges specifying basis sets and various other options Chapter 5 describes optimizations of the molecular structure transition state searches and geometry scans Chapter 6 describes how to summarize Jaguar output and the output or printing options avail able from the GUI The output file containing the primary Jaguar output is first described for cases where no Output options have been selected Next the output given when various Output settings are turned on is explained Finally the log file is described Chapter 7 contains tips and suggestions for using Jaguar The chapter includes some general tips for different sorts of calculations a description of how to restart calculations how to incor porate results from previous runs and some tips on using both Jaguar and GAUSSIAN Chapter 8 describes some of the theory behind the pseudospectral method and the electron co
520. uld like more information on input files Note that if you restart a run you may not get exactly the same results as you would if you had simply performed a longer run in the first place even if the calculation type is the same The methods used in Jaguar sometimes use data from previous iterations if this information is available but the data may not be stored in the new input file For example the DIIS conver gence scheme uses Fock matrices from all previous iterations for the run and Fock matrices are not stored in new input files However calculations should ultimately converge to the same answer within a standard margin of error whether they are restarted or not If your run aborted or was killed before completion and you want to restart the calculation or start another calculation where that one left off you can look for a file called restart in The file is located in a subdirectory whose name is the same as the job s and which is found within the temp directory for the job which was listed in the Start panel By default the restart in file is written out at the end of the Jaguar programs for calculating the initial guess performing the SCF iterations and calculating a new geometry for geometry optimizations as well as at the end of each SCF iteration To turn off restart in file genera tion the input file output keywords ip151 and or ip152 in the gen section should be set to 0 The restart in file is overwritten each time
521. ult data files used for the calculation see Section 9 1 on page 167 and Chapter 10 Next the basis set used for the calculation the molecule s net charge and multiplicity and the number of basis functions used for the calculation are specified This information is followed by the molecular geometry input which gives the atom label and coordinates for each atom If the atom labels provided in the geometry are not unique for instance if two hydrogens are each called h this information is preceded by a list of original atom labels and new atom labels assigned by the program The molecule s symmetry is analyzed a process which may involve translating and rotating the molecule These procedures are noted in the output file along with the point group used for the calculation the nuclear repulsion energy and the symmetrized geometry which is used for the rest of the calculation Jaguar 6 0 User Manual Chapter 6 Output One electron integrals are calculated by the onee program which prints the smallest eigen value of the overlap matrix S and the number of canonical orbitals used for the calculation Canonical orbital eigenvectors with very small eigenvalues less than 5 0 x 10 are removed and thus are not counted The eigenvalue cutoff can be controlled by setting the keyword cut20 to the desired value in the gen section of the input file The number of canonical orbitals can also be controlled by setting the keyword ncanorb
522. unctional groups and significant flexi bility We have not carried out an exhaustive analysis of the conformational energetics for these cases hence much of the deviation from experiment that we report may be due to this Never theless the errors are quite respectable Jaguar 6 0 User Manual 315 Chapter 14 The pK Prediction Module The largest overall error is that for alcohols This is to be expected because the experimental values themselves are subject to greater uncertainty Most of the pK values are higher than 14 so the leveling effect of hydroxide makes the determination of the aqueous pK difficult Table 14 1 Functional groups for which pKa parameters are available Maximum jres File RMS Absolute Group Functional Group Deviation Deviation Number ACIDS Alcohols 1 0 2 5 1 Phenols 0 2 0 3 2 Carboxylic acids 0 6 1 5 4 Thiols 0 4 0 6 10 Sulfonamides 0 7 1 5 15 Hydroxamic acids 0 6 1 4 6 Imides 0 9 1 5 13 Barbituric acids 0 2 0 4 12 Tetrazoles 0 6 1 4 17 BASES Primary amines 0 5 0 8 31 Secondary amines 0 5 0 9 32 Tertiary amines 0 4 1 1 33 Anilines 0 2 0 6 25 30 Amidines 0 3 0 5 22 Heterocycles 0 2 0 4 19 Benzodiazepines 0 3 0 3 23 Guanidines 0 5 0 8 21 Pyrroles C 2 protonation 0 2 0 3 35 Indoles C 3 protonation 0 2 0 3 36 316 Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module Table 14 2 Molecules used in the pK parametrization arranged by functional group MOLECULE pKa calc pK ex
523. urface area in A which reflects the surface formed from the points whose closest distance from the molecular surface is equal to the probe radius of the solvent and the cavity energy in kT which is computed to be the solvation energy of a nonpolar solute whose size and shape are the same as those of the actual solute molecule as described in reference 15 The output from the program solv follows the Poisson Boltzmann solver results giving the number of point charges provided by the solver to model the solvent the sum of the surface charges the nuclear repulsion energy already calculated by Jaguar the nuclear point charge energy representing the energy of interaction between the molecule s nuclei and the solvent point charges and the point charge repulsion energy which is calculated but not used by the rest of Jaguar because it is irrelevant to the desired solvation results After this output the output for the second solvation iteration begins The output from scf comes first giving the results for the molecule and solvent point charges system An example from the first solute with solvent point charges scf run in a calculation of 6 31G water in cyclohexane using the Jaguar solver is given here start of program scf i u d i g t p RMS maximum e d i u i energy density DIIS rts t d total energy change change error etot 1 NN 2 U 76 03588607997 6 8E 04 6 6E 03 etot ao Y Y M 76 03615425936 2 7E 04 1 9E 04 1 8E 0
524. using the keyword ifdtherm A value of 1 selects the FON method a value of 2 selects the pFON method You can use thermal smearing with the RHF ROHF UHF DFT RODFT and UDFT methods The number of alpha and beta electrons is kept the same during thermal smearing Thermal smearing can be used with or without symmetry and it can be used with the ipopsym keyword You can set the initial temperature using the fdtemp keyword The units of fdtemp are Kelvin The default initial temperature is 10 000 K The temperature decreases as a function of the rms density change When the density is close to the convergence threshold the temperature is set to zero The number of canonical orbitals kept in an SCF calculation is controlled by the cut20 keyword Eigenvectors of the overlap matrix i e canonical orbitals are discarded in a calcula tion if their eigenvalues are less than cut20 It may be necessary to fix the number of canonical orbitals during a calculation such as during a geometry optimization or scan or between calculations such as when comparing energies of related structures You can set the number of canonical orbitals with the ncanorb keyword and you can fix the number of canonical orbitals to the number determined for the initial structure by setting icanorb 1 When ncanorb is set to a value less than the number of basis functions the canonical orbitals with the lowest eigen values of the overlap matrix are discarded until there are ncano
525. ut Level of theory DFT Density Functional Theory DFT Spin unrestricted Grid density Medium _ Functionals Hybrid B3LYP wv Gradient corrected BLYP zi wv LDA Start Read Write Edit Reset Close Help Figure 4 2 The Theory folder showing DFT controls The most commonly used functionals can be selected from the option menus in the Functionals section There are three classes of functionals available local density functionals gradient corrected pure density functionals and hybrid functionals which include a Hartree Fock exchange contribution as well as local and nonlocal functionals Most of the hybrid methods employ either the parameters developed for Becke s three parameter method 27 28 Becke 3 or the parameters developed for Becke s Half amp Half method 26 The option menus also contain some recently developed hybrid and non hybrid functionals The functionals available from the option menus are described below Jaguar 6 0 User Manual Chapter 4 Options LDA Local Density Functionals Functionals with local exchange only HFS Slater local exchange functional 29 Xalpha Xa local exchange functional 29 Functionals with local exchange and local correlation SVWN Slater local exchange functional 29 Vosko Wilk Nusair VWN local correla tion functional 30 SVWN5P Slater local exchange functional 29 Vosko Wilk Nusair 5 VWNS local cor
526. ut The other folder available for pK calculations is the SCF folder in which you can make settings to control the SCF convergence Once you have selected the target molecule or molecules set the pK atom and adjusted any settings for the SCF convergence click Start and make job settings in the Start dialog box then click Start again to submit the job See Section 3 9 on page 46 for information on job settings You can distribute a job for multiple molecules across multiple processors When the pK jobs are incorporated on completion the pK value is added as a property to the Project Table The values are accurate only to the first decimal place although displayed to 6 14 4 3 Jaguar Input Files for pK Calculations You can prepare a Jaguar input file for a pK calculation using a text editor The input file must contain a molecular geometry and a labeled acidic site The acidic site is either an acidic hydrogen in acids or a heteroatom to be protonated in bases If the starting geometry is not a neutral molecule but an ion you have to specify its formal charge in the atomic section see Section 9 8 on page 226 Also if the geometry files are not in Jaguar format you can translate them using Babel see Section 11 2 5 on page 278 or type jaguar babel in a terminal window for usage instructions The acidic site can be marked using one of the following methods By adding the suffix _pk to the atomic symbol in the zmat section By
527. ut file as described in Section 9 5 15 on page 200 The orbital coefficients are always printed out in terms of the six Cartesian functions For basis sets with f functions the real spherical set of 7 f functions is always used The references describing the basis sets are in the References list at the back of this manual Table 4 1 Available basis sets that do not include effective core potentials Atoms of Basis Set Included Options Method dfns Refs STO 3G H Xe Na Xe analytic 5 65 69 3 21G H Xe Na Ar H Ar pseudospectral analytic 6 70 72 Li Ar with or K Xe analytic H Ar 4 21G H Ne ee analytic 6 23 6 21G H Ar Ber analytic 6 70 72 4 31G H Ne eae analytic 6 74 79 6 31G H Ar RS b pseudospectral 6 75 80 6 311G H Ar c 4 44 H Li C F Na Si Cl pseudo 5 82 85 spectral others analytic 6 311G 3df H Ar analytic 5 82 85 3pd 6 31G tm H Zn RR H Ar pseudospectral K Zn ana 6 75 81 for H Ar lytic m6 31G tm K Zn analytic 6 86 D95V H Li Ne quss analytic 6 87 D95 H Li Ne Ae o H Li C F Si Cl pseudospectral 6 87 Al Cl others analytic MSV H Ru Pd Xe analytic 5 88 cc pVDZ H He B Ne H C F Si Cl pseudospectral 5 89 92 Al Ar others analytic analytic cc pVDZ d H He B Ne H C F Si Cl pseudospectral 5 89 92 without d Al Ar others analytic analytic functions Jaguar 6 0 User Manual Chapter 4 Options Table 4 1 Available basis sets that do not i
528. ut their values for one hydrogen atom would always be the same as those for the other hydrogen atom so the molecule would retain C symmetry The variable settings can also be separated from the coordinates by a line containing the text Z variables For instance the following input is equivalent to the previous example Oo 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor Z variables ycoorz0 753108 zcoor 0 454006 Jaguar 6 0 User Manual Chapter 3 Running Jaguar From Maestro Note that if Cartesian input with variables is used for an optimization Jaguar performs the optimization using Cartesian coordinates instead of generating redundant internal coordinates and the optimization will not make use of molecular symmetry 3 4 3 Constraining Cartesian Coordinates As described in the previous section you can force Cartesian coordinates to remain the same as each other during an optimization by using variables You can also specify Cartesian coordi nates that should be frozen during a geometry optimization by adding a sign after the coor dinate values For example if you add constraints to the zcoor variables in the water input example as listed below 0 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 and perform a geometry optimization on this molecule the H atoms would be allowed to move only within the xy plane in which th
529. ve permission to create that directory if it does not already exist If you are unable to allow rsh commands as described above e g your local and execution hosts are not local to each other you must include the local machine in a rhosts file in your home directory on the execution host and vice versa If you have the same user name on both nodes a line in the rhosts file only needs to contain the entire host name For more informa tion see the rhosts man page on your machine One further complication can result if you have distinct user names on the local and execution hosts In this case you may get an error like one of the following Jaguar 6 0 User Manual 293 Chapter 12 Troubleshooting 294 Login incorrect remshd Login incorrect rshd xxxx xxxx The remote user login is not correct This problem generally occurs only when the local and execution hosts are on separate local area networks To handle these distinct sites you must use a personal schrodinger hosts file Each host line in the file should include your user name on that host in the following format host sgi username calculation hostname where the name of the machine in the host field matches that in the uname n command output for that machine username is replaced by your user name and calculation hostname is replaced by the name of your execution host See Section 11 1 on page 269 for details on how to construct your own schrodinger hosts fi
530. verted if no range is given otherwise the first structure is converted by default To generate a set of single structure files use the split keyword The names of these files have a four digit index number inserted before the file extension For example to write indi vidual Jaguar input files Cartesian for the 5th through 10th intermediate structures in a Jaguar geometry optimization run type the command jaguar babel ijagout job out 5 10 ojagc iter in split The files iter0001 in iter0002 in iter0006 in are written by Babel Babel cannot read Maestro formatted files To convert between Maestro format and some other formats a file utility called jagconvert has been provided For conversions between various Schr dinger file formats that are not recognized by Babel there is a file conversion utility jagconvert This utility reads and writes Jaguar input in files BioGraf bg files XMol xyz files and Maestro mae files It also reads Gaussian9x g9x files and MacroModel dat files but doesn t write them The utility is located in SCHRODINGER utilities The command syntax is as follows jagconvert intype infile outtype outfile where intype is one of ijag ixyz ibgf ig92 or imae and outtype is one of ojag oxyz obgf or omae The input file is assumed to be a Jaguar input file if no input type is explicitly given MacroModel files are read in using imae If you convert a file that contains mu
531. ween them is less than covfac times the sum of their covalent radii where covfac is a keyword with a default value of 1 2 These radii can be changed using the cov keyword See page 137 and Section 9 5 1 on page 174 for more information on how Jaguar uses and presents covalent radii and bonding information 9 8 3 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms The basis keyword allows you to specify the basis sets used to treat particular atoms The string provided to describe the basis set should be chosen from the first column of the tables in Section 4 2 Lowercase or uppercase letters can be used Polarization and diffuse functions can be added by appending or immediately after the basis name The meaning of these symbols is also described in Section 4 2 If you use an atomic section to specify different basis sets for one or more atoms than the basis set used for the other atoms in the input you should not change any basis set assignments if you later restart that job For instance if you run a job whose input file mixmol in contains an atomic section that specifies different basis sets for different atoms you can generate a new input file restart file called mixmol 01 in from the job but if you use this input file for a second job restarting the old calculation you may not change the atomic section at all other wise the program misinterprets the initial guess specified in the guess section in mi
532. which is described in detail in Section 9 10 on page 235 or for input to GAUS SIAN guess cards Here are some examples of output for each of these style options The output shown is from output files generated from a calculation of water with a 6 31G basis set for occupied orbitals after the SCF iterations Only the first two occupied orbitals are shown in each case and not all functions are shown these gaps are indicated by For the Format option Large elements as f5 2 labels in list 1 Orbital Energy 20 555133 Occupation 1 000000 Symmetry A1 S Oo 0 99 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 S S Z S Oo 0 21 0 47 0 09 0 42 S Hl 0 15 S H2 0 15 For the Format option All elements as f10 5 labels in table L 2 3 eigenvalues 20 55513 1 34560 x 10 S 0 99466 0 21055 20 S 0 02122 0 47102 ee 5 0 Z 0 00155 0 08586 6 0 S 0 00430 0 41777 16 Hl S 0 00000 0 14851 aoe 21 H2 S 0 00000 0 14851 Feas 25 H2 Z 0 00025 0 01342 Jaguar 6 0 User Manual 141 Chapter 6 Output 142 For the Format option All elements as f19 15 in list 1 Orbital Energy 994661070265476 001550431863529 000190485390547 000000000000000 000343482092802 000004988565650 000252040203901 2 Orbital Energy 210549363265932 085862488931510 031498167188452 000000000000000 013067257872503 148513692384474 r4 2995995 013419565122871 0 oooo0o0 2
533. wn to be sufficient for the present purposes some of the errors induced are compensated by the empirical parameterization As we have discussed extensively in several publications empirical optimization of parameters is absolutely necessary to obtain accurate solvation free energies from SCRF calculation no matter what the level of electron correlation Continuum solvation methods do not rigorously treat effects at the dielectric boundary which therefore must be adjusted to fit experiment For neutral species we have optimized parameters both dielectric radii and surface tension terms by fitting to experimental gas to water solvation free energy data for small molecules Agreement to within a few tenths of a kcal mole can be obtained for most functional groups However parameterization of the model for ionic species in this fashion cannot lead to high levels of accuracy because there are large error bars on the experimental data typically 5 10 kcal mole An error of 5 kcal mol in the solvation free energy that was not systematic would lead to huge errors in pK calculations This is because in determining the pK there is a cancel lation of two very large terms the gas phase deprotonation energy which favors the proto nated state and the solvation free energy which favors the deprotonated state Errors in either term therefore can be a small percentage of the total energy but lead to very large errors in the resulting calculated pK
534. ww caos kun nl schaft molden molden html Stewart J J P MOPAC 6 QCPE 455 Hohenberg P Kohn W Phys Rev B 1964 136 864 Kohn W Sham L J Phys Rev A 1965 140 1133 Parr R G Yang W Density Functional Theory of Atoms and Molecules Oxford New York 1989 Density Functional Methods in Chemistry Labanowski J K Andzelm J W Eds Springer Verlag Berlin 1991 Colle R Salvetti O J Chem Phys 1990 93 534 Kraka E Chem Phys 1992 161 149 Audi G Wapstra A H Nuclear Phys 1995 A595 4 409 Cs sz r P Pulay P J Mol Struct 1984 114 31 Schlegel H B J Comput Chem 1982 3 214 Jaguar 6 0 User Manual 341 References 342 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 Powell M J D Math Prog 1971 1 26 Bofill J M J Comp Chem 1994 15 1 Murtagh B A Sargent R W H Comp J 1970 13 185 Fletcher R In Practical Methods of Optimization Wiley New York 1987 Banerjee A Adams N Simons J Shepard R J Phys Chem 1985 89 52 Culot P Dive G Nguyen V H Ghuysen J M Theor Chim Acta 1992 82 189 Simons J Jorgensen P Taylor H Ozment J J Phys Chem 1983 87 2745 H ser M Ahlrichs R J Comput Chem 1989 10 104 Cremer D Gauss J J Comput Chem 1986 7 274 Alml f J Faegri K Jr Korsell K J Comput
535. xchange functional 29 BHandHLYP Exchange 50 exact HF exchange 50 Slater local exchange functional 29 correlation Lee Yang Parr local and nonlocal functionals 33 X3LYP Extension of B3LYP by Xu and Goddard to include Perdew Wang 1991 gradi ent correction exchange functional 31 with exchange parametrized to fit Gaussian exchange density 44 MPW1K Reoptimization of mPW1PW91 functional parameter for prediction of reac tion barrier heights by Lynch Fast Harris and Truhlar 43 Keyword dftname hcth407 in the gen section Keyword dftname b3lyp in the gen section Keyword dftname b3pw91 in the gen section Keyword dftname b3p86 in the gen section Keyword dftname b97 1 in the gen section Keyword dftname b98 in the gen section Keyword dftname sb98 in the gen section Keyword dftname bhandh in the gen section Keyword dftname bhandhlyp in the gen section Keyword dftname x3lyp in the gen section Keyword dftname mpwlk in the gen section Jaguar 6 0 User Manual Chapter 4 Options e MPW1PW91 Hybrid functional including modification of Perdew Wang gradient cor rection exchange functional by Adamo and Barone 42 Exchange Exact HF exchange Slater local functional 29 Perdew Wang 1991 gradient correction functional 31 cor relation Perdew Wang 1991 GGA II local and nonlocal functionals 31 The names of the functionals in this list are valid values of the keyword dftname which yo
536. ximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on core orbitals for LMP2 calculation maximizing Mulliken basis function populations loclmp2v 1 Perform Boys localization on valence orbitals for LMP2 calculation 2 Perform Pipek Mezey localization on valence orbitals for LMP2 calcula tion maximizing Mulliken atomic populations 3 Perform Pipek Mezey localization on valence orbitals for LMP2 calcula tion maximizing Mulliken basis function populations 9 5 7 DFT Keywords To use density functional theory DFT you should set the dftname keyword You can also use the idft keyword which was the only option in versions of Jaguar prior to 5 0 If you want to evaluate the non self consistent energy of the final post SCF wave function using a partic ular set of functionals you can use the jdft keyword Most DFT options described here are also available from the GUI as described in Section 4 3 on page 59 For information on setting the keywords associated with grids for DFT calculations see Section 9 5 24 on page 218 The dftname keyword can be given as a standard functional name as listed in Table 9 8 or it can be constructed from a set of functional name strings for exchange and correlation func tionals which are listed in Table 9 9 The corresponding values of idft are listed along with the functional name strings For example dftname bp86 specifies the BP86 functional and is a combination of b for exchange
537. xmol 01 in Alternatively you can delete the guess section completely and then change the atomic section Jaguar 6 0 User Manual 229 The Jaguar Input File Chapter 9 SSTT SPET PLUT ESET LET LLET OCFT O9 TL LAYI PEST 8 T OLST IST ISS T 6577 1g 8 4d C8 LL I8 8H OS8 hV 6LUd 8LI LL SO 9L PA SLIM vL L LJH CL I L6 d 96 5 ss TOTT OSTT SETT OIT T 9617 TETT vev I YLSI OSP TL VOV TL ISP T 66V TL OTST ESSI COST CLOT ICST L60 C x PSII eslar zejas sjus OSU 6b PO S8t 9V Lp Pd Op UN SPINA prL erjow CP QN IPZ or a 6 S selau LE ILOT S6O T COLT SITT OPET TOLT ISET SPLIT LIT 9cr 1 967p OSHT TIST CLOT L8S T Lv97T OOL T 9061 DI 9tJH SEPS v SV EEJOD CE D IC UZ O nO 6C IN 86 00 LTA OTUN SCHO CJA ETL TIPS Iced OTA 6I 8561 8961 OLOT LYTT LITT 80 C BOET 80 C Iv IJO LIS 9I d STS rvI IV El SIN CL N II 9 LTI 9EL T COLT I 8 1 6761 THOT ELEI IT I N Old 60O 8N L49 94 ed pI ISTI L6S I H 7 H I T6 QPI soDieuo pally dS jeuejod oejsojjoeje Jo uogejnojeo ui pesn swonsbuy ul Ipe sjeeM 49p UBA Et 6 algeL Jaguar 6 0 User Manual 230 The Jaguar Input File Chapter 9 SSTT srl PLUT ESET LOOT LLET OCFT O9 TL LAYI PEST 8 T OLST IST ISS T 6577 Id 8 dd c8 LL IS SH os nv 6L d 8LI LLISO 9L
538. y is available Density functional theory particularly the hybrid methods that include Hartree Fock exchange have been shown to provide good quality geometries we utilize B3LYP 6 31G geometry optimization Jaguar 6 0 User Manual Chapter 14 The pK Prediction Module 2 Accurate single point energies at each optimized geometry must be evaluated These sin gle point calculations are carried out at a significantly higher level of theory than the geometry optimization but since only one energy is required the overall cost of this step is less than that for geometry optimization In recent publications and in our own exten sive unpublished work the B3LYP method with large basis sets has been shown to yield excellent gas phase energetics for deprotonation reactions with errors typically in the 1 3 kcal mol range We use the cc pVTZ basis set of Dunning and coworkers in the present methodology The cc pVTZ 4 basis set represents a mixed basis set where cc pVTZ is used for atoms involved in the deprotonation reaction while cc pVTZ covers the rest The residual errors in the DFT calculations appear to be relatively constant for a given functional group as the substituents are altered and hence can be largely removed by the empirical corrections 3 The solvation free energy of the protonated and deprotonated species must be computed We have chosen to do this using the gas phase geometries an approximation that we have tested and sho
539. y a range of values for coordinate scans You can assign a list of values to the variable in the format at number list or you can assign the initial value specified by number or rom number and two values from the following list in the order given in the list The final value of the coordinate specified by to number The step size specified by by number The number of steps specified by in integer Here integer means an appropriate integer and number means an appropriate real number See Section 5 4 2 on page 100 for information and examples 9 4 The coord and connect Sections For some geometry or transition state optimizations you might want to specify that the opti mizer use particular internal coordinates For example if you study a bond forming reaction you can require Jaguar to use the bond in question as an internal coordinate even when the bond distance is very long You also might want to generate your own list of internal coordi nates for cases that involve multiple separate unbonded fragments It is often useful to specify internal coordinates for pairs of atoms that are on separate sections of a large floppy molecule but are close to being in van der Waals contact Otherwise small changes in a torsional coordinate far away from these atoms can then lead to steep changes in the energy Adding explicit coordinates for these non bonded contacts makes it possible for the optimization algorithm to control their approach
540. y atom x5 is between 3 and 1 angstroms atom x y z Oo 0 0000000000 0 1135016000 0 0000000000 Hl 0 7531080000 0 4540064000 0 0000000000 H2 0 7531080000 0 4540064000 0 0000000000 x4 0 3765540000 0 1702524000 0 0000000000 x5 0 3765540000 0 1702524000 0 0000000000 gridpoints used for charge fit 4162 out of a possible maximum of 4188 Electrostatic potential fitting constrained to reproduce total charge yes dipole moment no traceless quadrupole moment no traceless octupole moment no Atomic charges from electrostatic potential Atom O H1 H2 x4 x5 Charge 0 31208 0 63681 0 63681 0 48077 0 48077 sum of atomic charges 0 000000 RMS Error 8 26E 04 hartrees If the fit is constrained to reproduce the dipole moment or dipole and higher moments or any other time both electrostatic potential fitting and multipole moment calculations are performed new moments can be calculated from the fitted charges as described in Section 4 10 1 on page 74 The output from ch begins with the moments calculated for the quantum mechanical wave function in the format for multipole moment calculations Next the electrostatic poten tial fitting information is provided as described above Finally the components and totals of the moments recalculated using the electrostatic potential charges are reported Jaguar 6 0 User Manual 125 Chapter 6 Output 126 6 3 7 2 Polarizabilities and Hyperpolarizabilities If you calculate po
541. y file output keyword whose default value of 1 indicates that it is on When ip151 is set to 1 the file restart inis created in the temp directory for the job at the end of the last completed Jaguar program writing over any previously generated restart in file for the job The file restart in contains the results from the run including the new geometry if the run that produced it was a geometry optimization This input file can therefore be used to restart the calculation At the end of the job the restart input file is copied to your local job directory under the name jobname 01 in unless that file already exists otherwise jobname 02 in or jobname 03 in and so on To turn off ip151 you must set it to 0 Setting ip472 2 writes structures at each step of a geometry optimization or an IRC scan to the Maestro formatted output mae file The other file output keywords control whether files for various other programs such as GAMESS are written out during a Jaguar job The effect of setting each of these keywords to 2 is shown in Table 9 33 Many of these options can be turned on from the GUI as described in Section 6 5 on page 138 Additional settings are available for ip160 and ip165 When ip165 3 the SPARTAN 4 0 archive file is written to the local job directory as jobname arc When ip160 3 an initial guess is included in the gau file generated by the run by default gau files generated for GVB calculations include initial g
542. y in the input file as described in Section 9 1 on page 167 If the input file has no such entry Jaguar uses the file default cutoff from the data directory If the CUTOFFFILE entry is accurate cutoff solvent cutoff or quick cutoff the program interprets the setting as default cutoff The first line of a cutoff file contains a character string that includes the version number of Jaguar This should be cutv followed by four digits giving the version number times 100 Leading zeroes are added if necessary A comment on the same line can follow the version string Jaguar 6 0 User Manual 257 Chapter 10 Other Jaguar Files 258 The next five lines each have five numbers Each line describes a particular level of accuracy to be used for the calculation The first line provides the information necessary to run a calcula tion with all ultrafine pseudospectral grids and with tight cutoffs and corresponds to an accuracy level setting of Ultrafine from the GUI as described in Section 4 8 1 on page 68 or to the keyword setting iacc 1 in the gen section of the input file as described in Section 9 5 16 on page 201 The second line gives the parameters for the accurate level iacc 2 while the third line provides information for the quick level iacc 3 The last two lines are filled with Zeroes since they are required but are not yet used In each of these rows the columns describe which cutoff sets are used for various SCF i
543. y is listed in Hartrees and in kcal mol and the note below it reads either solvation energy not yet converged or stopping solvation energy converged depending on whether the solvation energy has changed by less than the Solvation convergence criterion which is described in Section 4 9 on page 71 If the solvation energy has converged the output from the sole program includes a line summarizing the solvation energy iterations and result The output from ch and post appears below the sole output If the solvation energy has converged the ch output reflects the system s final atomic charges If the solvation energy has not converged these charges and the Poisson Boltzmann solver s files generated by the post program are passed to the solver again and the solvation iterations continue as previously described until solvation energy convergence is reached Jaguar 6 0 User Manual 123 Chapter 6 Output 124 6 3 6 Geometry Optimization in Solution Geometry optimizations in solution contain output in the formats described in the previous two subsections but the optimization output and the solvation calculation output alternates as the calculation proceeds First by default Jaguar computes a gas phase optimized geometry for which the output is the same as that described above for a standard optimization Next the SCRE procedure is used to compute a wave function for the solvated system as for a single point solvati
544. y use for your machine Jaguar 6 0 User Manual 295 Chapter 12 Troubleshooting 296 Jaguar 6 0 User Manual Chapter 13 Parallel Jaguar The parallel implementation of Jaguar is based on MPI Message Passing Interface Jaguar can run on SMP symmetric multi processing shared memory architectures such as worksta tions that contain multiple processors and it can run on distributed memory architectures such as IBM SP clusters or Linux Beowulf clusters Jaguar can also run on clusters in which each node contains multiple processors The development of parallel Jaguar is discussed in refer ences 142 and 143 The following kinds of jobs can be run in parallel HF and DFT single point calculations in gas phase or in solution HF and DFT geometry optimizations in gas phase or in solution Closed shell LMP2 single point calculations If you want to compute analytic frequencies you probably should run your Jaguar energy calculation or geometry optimization first in parallel then use the restart job for a frequency calculation in serial mode Jobs that cannot be run in parallel mode include Jobs that use all analytic SCF methods LMP2 jobs other than closed shell single point calculations LMP2 jobs with more processors than LMP2 orbitals GVB and GVB LMP2 jobs CPHF hyper polarizability jobs Jobs with more processors than atoms pK jobs jobs that use the Jaguar batch facility 13 1 Instal
545. yall jaguar benzene in benzene dft in Cee P Fi pump Launch Directory Working Directory File Format Jaguar input Fr Selection zonel dyall jaguar Figure 3 5 The Jaguar Write dialog box If you want to use the settings for a series of calculations on different molecules you can write a batch script by choosing Jaguar batch script from the File Format option menu When you click OK a Jaguar batch script is created that contains settings gen section and batch commands but no geometry so that you can run this script with any geometry To make use of this script you can select Run Batch File from the Jaguar submenu of the Applications menu in the main window You can also use Maestro to export structures to a variety of formats using the Babel file conversion program see Section 11 2 5 on page 278 See the Maestro User Manual for more information on exporting structures 3 9 Running Jobs Maestro provides several ways of running Jaguar jobs You can select a task from the Jaguar submenu of the Applications menu make settings then start the job you can select a set of preexisting input files and run them as a single job by selecting Run Input Files from the Jaguar submenu or you can run a job using a preexisting Jaguar batch file with one or more structures as input by selecting Run Batch File from the Jaguar submenu Whenever you run a calculation with multiple structures as input that does not hav
546. yword esses setting in atomic section atomic properties setting in atomic espe 226 234 atomic units see units atomig file default tbt 243 description and format 248 249 specifying in input file 167 atoms COUNLEIPOISE ru nenne 40 233 pn Y 39 atoms selecting eene 21 23 AutosHelp race eee t tte terreni 28 333 B babel using to convert file formats 209 212 using to read input files Balloon Help eene basis file description and format 243 247 specifying in input file 167 basis functions contracted uueeeeeenseeeeesneneeeeneneennnnnn 132 133 derivatives of list in output 213 file containing eee 243 247 for individual atoms 229 230 in counterpoise calculations 40 170 keyword for printing 212 listing in output eene 129 Mulliken populations for 128 number of 55 110 249 oiii e 132 135 type as listed in output 141 uncontracted ssesseee 132 133 basis set 55 59 conversion to Jaguar format 247 diffuse functions 55 200 244 file containing eee 243 247 for individual atoms
547. yword ip11 2 in the gen section Keyword ip12 2 in the gen section Keyword ip192 2 in the gen section en Jaguar 6 0 User Manual 137 Chapter 6 Output 138 Overlap matrix The overlap matrix S for the basis functions is printed in five column blocks if this option is selected Since the matrix is symmetric the upper triangle is not printed One electron Hamiltonian The one electron matrices representing kinetic energy and the sum of kinetic energy nuclear attraction and point charge electron interactions is printed in atomic orbital space in five column blocks if this option is selected Since the matrices are symmetric the upper triangles are not printed Gaussian function list basis set By selecting this option you can print out information about the Gaussian functions that make up the basis set Gaussian function list derivatives By selecting this option you can print out information about the derivatives of the basis set functions in terms of primitive Gaussians The format and information is the same as that discussed for the Gaussian function list basis set option immediately above 6 5 File Output Options The options available in the Output folder of the Jaguar panel under Write input files in the selected formats are described in this section These options are presented as a list from which you can select multiple items with the SHIFT and CTRL keys These output options generate
548. zability keywords l in file see input file included entries sisisi iesenii tsismis 15 infrared intensities sssessssss 83 200 OUtpUt i inne em rete 131 initial guess antiferromagnetic esss 148 234 choosing type 145 146 file information for 243 248 249 GVB from HF wave function 206 Improving n retten 147 148 information in output 111 input file section for 235 236 keywords erret 206 orbital output in format for 141 217 output of GVB inisio 216 printing orbitals after 139 216 restarted calculations s 146 stopping after 152 206 transition metal systems 145 146 147 148 impit Meee mern niei 167 170 defining fragments 233 234 description of sections 168 170 echoing in output file 135 239 ediUng eati ene uduluidius 243 GEN SECHON eic meta tee deri ise 153 general description and format 167 170 in jaguar run command 275 277 keywords ntt 174 220 MAME iss 277 reading in Maestro 41 42 restanto c ineo werten ee ine 150 151 CUP ET 45 46 section delineators sss 168 selecting in Maestro 51 spacing characters 168 summary of sections esee 169 input file sections Penn 226 234 inis M 172 174 C
549. zation except when Jaguar determines that changing it will lead to better convergence for problem jobs This setting is the default for optimizations to minimum energy structures If the trust radius is allowed to vary the default for transition state optimizations Jaguar keeps geometry changes within the region that is well described by the Hessian by increasing the trust radius when the Hessian is correctly predicting energy changes and decreasing it when the predictions are inaccurate Table 9 20 Keywords for trust radius adjustment Keyword Value Description itradj 0 Use same trust radius throughout optimization default for minimum energy structure optimizations 1 Adjust trust radius using Culot Fletcher heuristic 128 130 default for transition state optimizations 1 Adjust trust radius using Simons cubic potential model 131 not rec ommended with Jaguar itrcut 0 Apply trust radius by truncating Newton Raphson step s 1 Apply trust radius by level shifting of Hessian to reduce resultant step size trust 0 3 Initial trust radius in atomic units bohr and or radians if norm of pro posed displacements exceeds trust radius step size is reduced as described by itrcut default is 0 3 except for solvated cases or transition state optimizations when it is 0 1 tradmx 0 3 Maximum trust radius allowed during optimization for itradj gt 0 see trust information default is 0 3 except for solvated cases when it
550. zed orbital is considered to be localized on that single atom and that localized orbital will be included in any LMP2 calculation for which that atom is specified in any requested LMP2 atom pairs Jaguar includes a setting for a local LMP2 calculation that treats all atoms bonded to atoms of other elements heteroatom pairs at the LMP2 level These heteroatom pairs do not include C atoms bonded only to C and H atoms so hydrocarbon fragments are not correlated We recommend this setting for solvation calculations using LMP2 To request such a calcula tion select Hetero atom pairs in the LMP2 pairs section For other kinds of local LMP2 calcu lations you must set up the pairs in an Imp2 section by editing the input file See Section 4 5 on page 63 for more information If you add an Imp2 section the Level of theory is set to Other 36 Keyword loclmp2v 2 in the gen section 37 Keyword loclmp2v 1 in the gen section 38 Keyword loclmp2v 3 in the gen section 39 Keywords iheter 1 in the gen section Jaguar 6 0 User Manual Chapter 4 Options Jaguar jaguar EEx Use structures from Workspace included entries 1 Molecule Theory scr Properties Solvation Output Level of theory LMP2 Local MP2 r LMP2 Core localization method None at Valence localization method Pipek Mezey Resonance None m LMP2 Pairs All atom pairs w Hetero atom pairs Start Read Write

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