Home

GAMESS-UK USER'S GUIDE and REFERENCE MANUAL Version

1. criteria for grouping not met grouping atoms 5 to 7 not effected 6 points found on input of which 6 polarisable 13 DRF DIRECTIVES constructed 7 charged points 3 point polarisabilities and 1 group polarisabilities classical system specification name group wigri h wigri h wigri o wigr1 XX w2gr2 XX w2gr2 XX w2gr2 x 459378 459378 459378 459378 459378 459378 459378 www www Points to note 1 grouping the first molecule has succeeded all criteria 5 5 5 4 4 5 5 y 092418 595494 595494 492394 492394 595494 595494 RROORRO 000000 432500 432500 000000 000000 432500 432500 charge 0 0 O 0 0 0 O are the same as for the forced grouping 000000 398000 398000 796000 796000 398000 398000 47 radius alfa b 3 effalf b 3 analysis NNWNNDN W 542 267 267 872 100 500 500 are met wwoooo Oo 678 000 000 000 400 200 200 wwnnwwoao 000 469 469 817 400 200 200 PRPRPRPRPR PR and the resulting attributes 2 grouping of the second molecule was not effected because the induced dipole criterion was not met and the atoms are left as on input 3 no separate analysis of the interactions of the two molecules will be made it is not possible to specify an analysis group without forced grouping through the GROUP
2. tions between atoms The directive consists of a single data line read to the variables TEXT GROUPOPT NGRNAM1 NGRNAM2 using format 24 21 1 TEXT should be set to the character string GROUPING 2 GROUPOPT can be set to the character strings ON or OFF 3 NGRNAM1 is the number of characters at the start of the group name considered for exclusion of interactions 13 DRF DIRECTIVES 39 4 NGRNAM2 is the number of characters after the name considered for exclusion of interac tion considered for attempting to group atom polarizabilities to a group polarizability The default is GROUPING OFF 2 2 NOTE The GROUPING directive and the following grouping criteria are ignored if the user forces grouping of certain atoms This may be done within the EXTERNAL data block by entering a data line reading GROUP following a number of atoms See also the EXTERNAL directive NOTE NGRNAM1 specifies the number of characters considered from the classical atoms group name to exclude electrostatic dispersion and repulsion interactions between classical atoms The NGRNAM2 characters of the group name from NGRNAM1 onward are considered when decid ing whether to construct a group polarizability from the preceding atom polarizabilities Any remaining characters may be used for additional labelling of the classical atoms The energy does not depend on these remaining characters NOTE The names of the classical atoms are stored in a 16 character string the
3. LINE lineprinter plot CONT contour plot SURF surface plot 6 24 Plot Requests TITLE Provide a title for the plot TITLE title 6 25 Plot Requests TYPE Specify the type of graphical output required Valid directives are given in Table 3 6 26 Plot Requests CONT Set the contour heights for lineprinter and contour options The directive is followed by one or more records containing the values required terminated by end CONT cont 1 cont 2 END If the CONT directive is omitted the default set of contour values given in Table 4 will be used Contour values of POTE AMPLITUDE ATOM and DIFF setting also have corresponding negative values 6 27 Plot Requests VIEW The VIEW directive is only relevant when generating perspective plots and may be used to specify the angle of view and viewing distance The grid of electron densities or potentials define the z values of the surface on a two dimensional x y grid of points covering the specified area of the molecular plane under investigation The directive consists of a single data line read to variables TEXT THETAV THETAH and DIST using format A 3F 6 GRAPHICAL ANALYSIS 24 Table 4 Default Contour Values in Graphical Analysis GTYPE setting POTE DENS AMPLITUDE ATOM or DIFF 210 0 64 7837 1 0 0 8691 180 0 16 1959 0 5 0 43455 150 0 4 0490 0 25 0 21727 120 0 1 0122 0 125 0 10864 90 0 0 5061 0 0625 0 05432 75 0 0 2531 0 03125 0 0271
4. 5 092418 0 000000 0 000000 3 542 9 678 0 000 1 h w1 3 459378 5 595494 1 432500 0 398000 2 267 0 000 3 469 1 h w1 3 459378 5 595494 1 432500 0 398000 2 267 0 000 3 469 1 o w1 3 459378 4 492394 0 000000 0 796000 2 872 0 000 5 817 1 group w2gr 3 459378 4 969410 0 000000 0 000000 3 688 10 925 0 000 2 h w2 3 459378 5 595494 1 432500 0 398000 2 500 0 000 3 200 2 h w2 3 459378 5 595494 1 432500 0 398000 2 500 0 000 3 200 2 o w2 3 459378 4 492394 0 000000 0 796000 3 100 0 000 8 400 2 Points to note 13 DRF DIRECTIVES 46 1 a warning is given that the grouping may not be of enough accuracy to be justified The criteria are given in the directives AGRE AGRPM and AGRPC the group centres head the group members the first member of the group on input is now the last atom in the group The first part of the centre s group name w1 is inherited from the first atom the second part gr is added internally in the absence of further group name input the radius of the group centre is calculated from the group polarizability and depends on the settings of the directive DAMPING the radii and polarizabilities of the first water molecule are taken from internal data bases and depend on the settings of the directives CLASRADI and DAMPING respectively the radii and polarizabilities of the second water molecule are taken from input overriding any internal settings The group polarizability is however constructed under the settings of the
5. B D Olafson D J States S J Swaminathan and M Karplus J Comp Chem 4 1983 187 doi 10 1002 jcc 540040211 8 B T Thole Chem Phys 59 1981 341 doi 10 1016 0301 0104 81 85176 2 9 B T Thole and P Th van Duijnen Theor Chim Acta 55 1980 307 doi 10 1007 BF00549429 10 B T Thole and P Th van Duijnen Chem Phys 71 1982 211 doi 10 1016 0301 0104 82 87020 1 11 M L Connolly Science 221 1983 709 doi 10 1126 science 6879170
6. For 2 and 3D regular grids this sets the number of points along the axes For spherical grids the number of longitudinal and latitudinal divisions should be given as a single integer argument POINTS nx lt ny lt nz gt gt 6 10 Grid Definition SECTION Specify a section number isect on the dumpfile where the grid is to be stored SECTION isect Storage of the grid is required in the following circumstances e the grid is to be restored later in the job or in a later GAMESS UK run e the grid is irregular ie a type other than 2D or 3D and is required to appear on the punchfile along with data calculated on the grid 6 11 Directives Requesting Data Calculation 6 12 Data Calculation CALC The computation of data on a predefined grid is requested by the CALC directive All subsequent directives up to the next GDEF CALC PLOT SURF REST or other Class 2 directive serve to specify details of the calculation CALC 6 GRAPHICAL ANALYSIS 14 Table 2 Keywords of the Data TYPE Directive keyword Data Type MO Molecular Orbital DENS electron density ATOM atom difference electron density POTE electrostatic potential GRAD DENS gradient of the charge density GRAD MO gradient of MO COMB linear combination with the previous calculation VDW Van der Waals function LVDW log Van der Waals function GRAD VDW gradient of Van der Waals function GRAD LVDW gradient of Van der Waals function sic 6 13 Data Calculation T
7. GRID TYPE 3D POINTS 60 SIZE 8 0 CALC TYPE DENS SECTION 150 SURF POTE 160 0 02 0 04 VECTORS 1 ENTER The result would be following job steps 1 A 3D grid with edge length 8 a u centred on the origin is defined 2 The density is calculated at all points on the grid and written to dumpfile section 150 3 A set of points on the surface of electron density 0 02 are generated and written to dumpfile section 160 4 The gradient of the density is calculated at each point and written to dumpfile section 161 5 The potential is calculated at every point and written to section 162 6 The 3D density grid is restored from the dumpfile 7 Steps 3 4 and 5 are repeated for a density value of 0 04 resulting in the new grid definition being written to section 163 that density gradient to section 164 and the potential to section 165 8 The data from sections 161 162 164 and 165 are written to the punchfile The grid definitions from sections 160 and 163 also appear on the dumpfile although not explicitly requested 6 22 Plot Requests Note that Users of versions of GAMESS UK which support GHOST graphics can generate contour plots TYPE CONT and relief plots TYPE SURF Otherwise only lineprinter plots are available 6 23 Plot Requests PLOT Plots are requested by a series of directives initiated by the PLOT directive 6 GRAPHICAL ANALYSIS 23 Table 3 Keywords of the Plot TYPE Directive keyword Data Type
8. PROPERTY ATOMS DIRECT 16 8 14 CONF 22222222 NATORB 10 O PRINT ENTER To further illustrate property evaluation for Cl wavefunctions let us consider a Cl calculation on the 3A state of H2CO First the data for the open shell SCF calculation TITLE H2C0 DZ BASIS 342 GRHF TOTAL ENERGY 113 73954029 AU MULT 3 SUPER OFF NOSYM ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END BASIS DZ OPEN 1 1 1 1 ENTER Having generated the SCF wavefunction the following data sequence would be used for a single reference Cl calculation routing the spinfree and spin natural orbitals to sections 10 and 11 of the Dumpfile will permit subsequent property generation requested by presenting the data line PROPERTY ATOMS RESTART NEW TITLE 5 LOCALISED MOLECULAR ORBITALS 7 H2C0 DZ BASIS 342 CISD DIRECT CI 113 934177537 AU MULT 3 SUPER OFF NOSYM BYPASS SCF ZMATRIX ANGSTROM Cc 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END BASIS DZ RUNTYPE CI PROPERTY ATOMS OPEN 1 1 1 1 DIRECT 16 9 15 SPIN 3 CONF 222222211 NATORB 10 11 PRINT ENTER Note that properties could also have been calculated after the Cl job by specifying the appropri ate natural orbitals under RUNTYPE ANALYSE The data below would compute the isotropic ESR coupling constants property index 19 at carbon oxygen and hydrogen where the spin NOS are nominated on the VECTORS line RESTART NEW TITL
9. atom atom overlap populations and sub dividing the orbital electrons into s p and d character say on the component atoms Such an analysis may be requested under control of the MULLIK directive 8 1 MULLIK This directive consists of a single data line and is used to define those molecular orbitals for which a detailed analysis is required and to define the type of analysis to be performed 8 MULLIKEN ANALYSIS 27 The first data field consists of the character string MULLIK One or two data fields may then be read in A format to define the type of Mulliken analysis required This analysis is performed by initially assigning basis functions to groups and then performing the Mulliken analysis over these groups rather than over individual basis functions Two such groups are recognised by the program and may be activated by appropriate keyword setting on the MULLIK directive The groups with appropriate keyword settings are as follows e Specifying the keyword ATOM will assign all basis functions sited on a given atomic centre to the same group with the group labelled by the centre name based on that specified by the ZMATRIX or GEOMETRY directive This will culminate in an atom atom type of Mulliken analysis e Specifying the keyword ORBITAL will provide a more detailed analysis than above with the atomic groups further classified into sub groups of specific orbital s p d or f character Subsequent data fields are used to s
10. ba Soe ee 6 26 Plot Requests CONT 2 2 20 02 a 6 27 Plot Requests VIEW 1 ee 6 28 Plot Requests SCALE a a a a a 6 29 Termination of GRAPHICS Input o o e 7 Potential Derived Charges 8 Mulliken Analysis Oa MUELIS 2 o cee Chie ee od oer eS ee EE Er nd bene 9 Distributed Multipole Analysis gk ADD aa Ae an Ben de SO A BA BOE OR a ded SE DELETE 40 24 54 4420 9504 66 55 64084 A DS RADIUS aie be ar oe eeh ene Bee ew EEO ETE ELSES DA AI is he eee as Soe ee Se ESS De es Oe SMETE be ek Aa Be e eS Do CAS ee NeR OER RES ES SRE WHEE HE OES Keek 97 GAUGE o nea Re ee Gwe EERE AA ARAS OF NONUCLEAR 226 eere cee ee ee Hoos OES Oe OES we ES es 10 The DRF Model for Solvation 11 Total energy in the DRF model 12 Features of the DRF Model 12 1 Grouping of External Points lt c s cs 2 ee 12 2 Damping Functions 2 6 255452 abe RRR Ree 4 12 3 CHARMM Model Repulsion 2 2 ee 12 4 Estimate of the Dispersion Interaction o e o iii 20 20 21 22 22 23 23 23 23 24 25 25 26 26 28 28 28 28 29 29 29 29 29 30 31 CONTENTS lv 125 Expansion of Fields saas a a a ge a eR 34 12 6 Dielectric Response 35 13 DRF Directives 35 E tn en ee een ee dee B ie en rr 36 INET a sarmi O A a he 36 A A a ed a ee hete 36 13 4 GAMDRE Conv are eeen a na ea de ade 37 ISO INCEROE lt a mone ya el ade a ce eo Rl eel 3 37 13 6 EXPANDCM 22
11. considered again NOTE The group name of the resulting group centre inherits the group name of the first atom in the newly formed group the group centre gets this atom s index and this atom is then put down as the last member of the group 2 x y z coordinates Cartesian co ordinate input for classical atoms is supported only 3 polarizability Atomic polarizabilities may be specified optionally If not specified default values are used according to the chemical symbol and the setting of the shape function used for damping potentials see section 12 2 NOTE if the potentials are undamped the polarizabilities associated with the conical shape function will be used 4 radius Atomic radii may be specified optionally If not specified default values are used according to the chemical symbol under control of the CLASRADI directive see above NOTE the radii are used in the CHARMM repulsion expression and for definition of a Juffer or Connolly surface if such a surface is requested see the DIELECTRIC directive Within the EXTERNAL block one other directive may be specified to force grouping of the preceding polarizabilities 13 DRF DIRECTIVES 45 GROUP ANAL n Forces construction of a group polarizability from the preceding atoms following the previous group This directive supersedes the formation of groups on the basis of group names see above Thus a GROUP directive placed within a series of atoms with th
12. dipole moments and surface polarisation by the charges in the analysis group only when A B 3 energies associated with the interaction between QM and classical system collected per analysis group nuclei external charge interaction electrostatic interaction between all QM nuclei includes any BQ centres with a charge and all charges in the analysis group electrons external charge interaction electrostatic interaction between all electrons and all charges in the analysis group screening of the ext charge nuclear int n interaction of all nuclei including BQ charges with the RF induced by all charges in the analysis group screening of the ext charge electron int n interaction of all electrons with the RF induced by all charges in the analysis group 14 DRF OUTPUT ANALYSIS OF D RF ENERGIES 55 ATA 4 total a b screening of the nuclei ext charge int n interaction of all charges in analysis group with the RF induced by all QM nuclei including BQ charges screening of the electron ext charge int n interaction of all charges in analysis group with the RF induced by all electrons electrostatic qm classical interaction sum of first 2 terms screening electrostatic qm classical int n sum of last 4 terms model repulsion energy CHARMM model repulsion energy between QM system and all atoms in analysis group energies associated with the interaction between QM and classical system as for individual analys
13. directive 4 the energy of the classical system and the interaction of the classical system with the QM system will be different for cases 1 and 2 for the following type of interaction a dispersion between classical subsystems this is because an XX centre is assigned 1 In case 1 one of the XX centres is an O with 6 rather than 1 valence electron valence electron repulsion between classical subsystems again this is due to the assignment of just 1 valence electron to XX induction and polarization energies this is because in case 2 the polarizability of the second molecule is represented by a distributed rather than group polarizability This will affect the response of the system dispersion energy between QM and classical system this is again because of the difference in response of the classical system 13 19 DIELECTRIC The DIELECTRIC directive specifies the options for the dielectric continuum It consists of a block data structure terminated by an END directive Below follow the descriptions of the DIELECTRIC subdirectives 13 DRF DIRECTIVES 48 13191 SURFACE The SURFACE directive serves to specify the type of surface enveloping QM and classical atoms to be constructed The directive consists of a single data line read to the variables TEXT SURFOPT using format 2A 1 TEXT should be set to the character string SURFACE 2 SURFOPT is the type of surface to be constructed The following options are va
14. directive consists of a single data line read to the variables TEXT n INTOPT using format nA 1 TEXT should be set to the character string CLASCLAS 2 INTOPT may be either blank or one or more of the keywords ELST NOELST REPN NOREPN DISP or NODISP to switch calculation of the electrostatic repulsion and dispersion interactions between the classical fragments on or off respectively The default is CLASCLAS ELST DISP REPN 13 21 HBOND The HBOND directive serves to specify the use of the special CHARMM repulsion parameters for H bonds The directive consists of a single data line starting with HBOND which may contain a number of keywords followed by their values The HBOND keywords are 14 DRF OUTPUT ANALYSIS OF D RF ENERGIES 53 1 ON or OFF to switch special H bond repulsion on or off respectively 2 RADI to set the H atom radius used in CHARMM expression when within H bond distance 3 DIST to set the distance within which H bond radius is used The default is HBOND OFF Specifying HBOND ON is equivalent to HBOND ON RADI 1 0 DIST 4 5 13 22 DRFTWOEL The DRFTWOEL directive serves to specify the treatment of the 2 electron reaction field integrals The directive consists of a single data line read to the variables TEXT INTOPT using format 2A 1 TEXT should be set to the character string DRFTWOEL 2 INTOPT may be either blank or one of the keywords a DIRECT 2 electron RF integrals are calculated on the fly
15. is equivalent to examples 3 and 4 Example 6 LOCAL 2 TO 7 9 TO 14 END Note During the localisation process under control of RUNTYPE ANALYSE symmetry adaptation is automatically switched off to enable orbitals of different irreducible representation to mix although the total wavefunction remains of course a unitary transformation of the SCF wave function Assuming these orbitals are to be used in a subsequent SCF or GVB calculation via the VECTORS directive then the ADAPT OFF data line must be presented in any such job that utilises the LMOs Failure to provide such a line will probably lead to an error condition when restoring the vectors 6 GRAPHICAL ANALYSIS 10 6 Graphical Analysis 6 1 Introduction GAMESS UK supports the graphical analysis of wavefunctions by the calculation of charge densities molecular orbitals atom difference densities and electrostatic potentials on a grid of points Versions of GAMESS UK which are linked to the GHOST graphical library allow graphical display of those datasets which are calculated on regular two dimensional grids as contour or surface plots In general the data values will be written to the formatted punchfile See Part 11 and analysed using other visualisation software The module is invoked under control of RUNTYPE ANALYSE by presence of the GRAPHICS directive Unlike the graphical analysis code present in previous versions of GAMESS UK the GRAPHICS keyword may only appear once f
16. of a calculation 2 APLOT directive must be preceded directives to generate or restore a suitable array of data values to be plotted 3 A SURF directive must follow the generation or restoration of an array of scalar data points on a regular 3D grid 6 GRAPHICAL ANALYSIS 11 Table 1 Keywords of the Grid TYPE Directive keyword Grid Type 2D Planar Rectangular 2D grid 3D Orthogonal 3D grid SPHERE Spherical grid CARDS User specified points CONTOUR Generate points on an isovalue surface WRAP Generate points on an iso electron density surface ATOM Place grid points at the nuclear positions All directions and positions specified must be given in the molecular coordinate system after reorientation by the GAMESS UK symmetry routines in units of a u At present the number of grids the number of calculations the number of plot requests and the number of dumpfile restore operations are each limited to 10 this total including requests made implicitly by SURF directives see below Users who need to generate more data may use multiple sets of directives starting with RUNTYPE ANALYSE 6 2 Grid Definition Directives 6 3 Grid Definition GDEF GDEF Grid definition mode is initiated by a GDEF directive This may optionally be followed by by a Character string 8 characters or less which will be used in the output to reference the grid Grid definition mode is terminated by a GDEF CALC PLOT REST SURF or va
17. 4444446404 646444 A ee a e ad 37 IST ASSIGN sea dat creek 6 eee de Se ae Be tee A Eman an oe a 38 188 GROUPING lt er tee dan Aden ee dk el de zo 38 13 9 DSTGRP an ca aa a ar A ree ee en dee ER g 39 IZ AUDE TIVA en oa a A ek Am ek le Bt Se he See ali 39 ISTUISGRPE eenn tate a ke We Sa eve bb Guam amp SH Gee eed 40 TSA ZAGRPM e a So wih a A era ce ee a ae de A amp 40 ISASAGRPG 4854454454844 044 34 ob bebe debe e eee ee OS 40 Ts LA AING gt sn tdi a A ew A ay a ee eee Betr oe ee E 41 1 ISCLASDISF En 41 13 16QMRADI 2 ee 42 ISAITELASRADI cod ek dee er ae Be ack a aw a 42 IS ABEXTERWAL 2 244 544 5465 68 baw Bhat SA ee da 43 IS JO DIBLECTRIG gt ecr p eek eB Pa eh GS a RE eee ee a are ds 47 TS WOU SUREACE 2 6 oen 260 24 b 6 rd eed irak da eee et 48 SAD ESRADIUS 25 ash hy Bs EN Se ee ai EE 48 1319 SEEMLEV og och ow Ae a ROS ede aa ee daa 48 TEAS AIUPPER ose eave ek a de we aud Gt el AAA 49 1319 BEONNOLES nn en ea tele ee a ee cw a A 49 13 AG GSOLVENT s ped casa db bw eae be ee ee ee g 50 DELETE i es he a ee ee ee ea a Kn 50 TRAD SOIEUOUT te ish ea he aie BG a lede ed 51 TS AG DEPSSTAT essa er bear Ro eee a ew a 51 TS AS MEPSOPT e ne ea ee aa ge BO no EH wl Ae 51 TOAD PN neen E A 52 CONTENTS v TE IG AAP PAD ora pou OS a Whe A AA 52 IZ20CLASCLAS ce ade a BR A Be Ak A ai 52 WEET lt sosoca e RA AA a e a a Ae ke h 52 US OUR ET eke s 0 a A A ad 53 14 DRF Output Analysis of D RF Energies 53 1 INTRODUCTIO
18. 6 60 0 0 1265 0 01562 0 01358 40 0 0 0633 0 00781 0 00697 20 0 0 0316 0 00391 0 00339 10 0 0 0158 0 00195 0 00170 5 0 0 0079 0 00098 0 00085 2 0 0 0040 0 0049 0 00042 0 0 0 0020 0 0 0 0 0 0010 e TEXT should be set to the character string VIEW e THETAV specifies the elevation of the view axis above the horizontal base plane in degrees e THETAH specifies the rotation of the vertical axis through the centre of the grid in a clockwise direction in degrees For 0 0 lt THETAH lt 180 0 the surface appears to rotate in a clockwise direction as THETAH increases e DIST specifies the viewing distance in Bohr If the VIEW directive is omitted THETAV thetav and THETAH thetah will be given the value 30 and DIST will be set to the value of SIZE specified by the PLANE directive Example To view the surface edge on along the y axis from a distance of 10 Bohr the following data line should be specified VIEW 0 0 0 0 10 0 6 28 Plot Requests SCALE This directive is only relevant when generating perspective plots and may be used to normal ize the stereo graphic projection to certain values of electron density or potential function The directive consists of a single data line read to variables TEXT SCAMAX SCAMIN and FACTOR using format A 4F 7 POTENTIAL DERIVED CHARGES 25 e TEXT should be set to the character string SCALE e SCAMAX FACTOR the grid of values to be plotted is scanned to detect all local maxim
19. CONTENTS i Computing for Science CFS Ltd CCLRC Daresbury Laboratory Generalised Atomic and Molecular Electronic Structure System ne GAMESS UK USER S GUIDE and REFERENCE MANUAL Version 8 0 June 2008 PART 8 WAVEFUNCTION ANALYSIS and MODELS for SOLVATION M F Guest J Kendrick J H van Lenthe P Sherwood and A H de Vries Copyright c 1993 2008 Computing for Science Ltd This document may be freely reproduced provided that it is reproduced unaltered and in its entirety Contents 1 Introduction 1 2 Analysis Modules Introduction 1 3 One electron Properties 2 3L PROPERTY ee enten Og ok eed Eo ds Be RE a Ble dens 2 332 CENTRES ana zer meden Den oc ee Be EK En a 4 2 33 NUCLIDI ec oe eemnes dh Bn ad 2 4 Simplified Property Specification 3 AA SCF Calculations zes oomen na ded heren Bin a ME e dead AD UHF Calculations c z s a2 60 0 ane Dame a ek a A Soe ce a CONTENTS 43 4 4 5 1 6 1 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 10 6 11 6 12 6 13 6 14 6 15 6 16 6 17 6 18 6 19 MP2 Calculations 60 5 6 g e an nne a a et a tene i BEEN EEn Localised Molecular Orbitals LOCAL tek de ee ee Od Bk hbe ok er dead Graphical Analysis REPSOUEHEN 2 2 sca e bee a ee EE wae Etn a E p ees Grid Definition Directives o c en Grid Definition GDEF een Grid Definition TITLE te p aa dee a ene Doe ee Hr en ER Grid Definition TYPE saes aa one a el a alen e a 651 TYPE SD or TYPE AD 2 cc hb ao
20. DAMPING directive as is the radius of the group centre the values of alfa are the mean polarizabilities used in calculation of the relay matrix to yield induction and polarization terms For group polarizabilities the polarizability tensor need not be and in general isn t isotropic the values of effalf are the mean polarizabilities that are used in calculation of the dispersion interaction between the classical subsystems The effective polarizabilities used need not be isotropic Their value and use depend on the settings of the CLASDISP directive In this example the isotropic atomic polarizabilities as given on input are used The default is CLASDISP ATOMPOL ORGPOL ISODIS the water molecules are put into two analysis groups 1 and 2 This will lead to final output in which the interaction between the first and second molecule is separated out as is true for their respective interactions with the QM system 2 The following EXTERNAL input is processed under the GROUPING ON 2 3 and DSTGRP 5 0 directives with other directives at their default values external o h h XX XX XX end w2gr2 0 398 wigr1 0 796 3 459378 4 492394 0 0 wigr1 0 398 3 459378 5 595494 1 4325 wigr1 0 398 3 459378 5 595494 1 4325 w2gr2 0 796 3 459378 4 492394 0 0 8 4 3 1 w2gr2 0 398 3 459378 5 595494 1 4325 3 2 2 5 3 459378 5 595494 1 4325 3 2 2 5 The relevant part of the output is induced dipole criterion for grouping not met
21. E H2C0 DZ 3A2 UHF SPIN DENSITIES MULT 3 ZMATRIX ANGSTROM N C D 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END BASIS DZ RUNTYPE ANALYSIS PROPERTY 19 C 190 19 H END VECTORS 11 ENTER 5 Localised Molecular Orbitals The purpose of this module is the localisation of molecular orbitals according to either e the criterion of Foster and Boys 3 5 LOCALISED MOLECULAR ORBITALS 8 e the overlap based criterion due to Pipek and Mezey 4 The particular technique to be employed together with the specification of the orbitals involved is requested by presenting the LOCAL directive 5 1 LOCAL This directive which may comprise one or more data lines is used to define those molecular or bitals which take part in the localisation process and the localisation technique to be employed The first data line comprises one or more data fields e The first field consists of the character string LOCAL e lf specified the second data field may be used to nominate the localisation technique to be employed and comprises the character string BOYS for the Foster Boys technique or OVERLAP for the Pipek Mezey overlap based method In the absence of this data field the default Foster Boys method will be used e f specified the third data field may be used to define a default set of orbitals to be incorporated in the localisation process Presenting the data field DEFAULT instructs the program to consider
22. H 11 1 2 109 0 END RUNTYPE SCF ENTER RUNTYPE ANALY GRAPHICS GDEF TYPE 3D POINTS 50 SIZE 6 SECTION 150 CALC 8 MULLIKEN ANALYSIS 26 TYPE DENS SECTION 151 TITLE DENSITY ON 3D GRID SURFACE POTE 170 0 02 0 04 VECTORS 1 ENTER RUNTYPE ANALY POTF 172 175 CHAR 0 0 VECTORS 1 ENTER This job consists of three phases each terminated by an ENTER directive e perform an SCF calculation writing vectors to Dumpfile section 1 e generate the electron density on a 3D grid and calculate the electrostatic potential at the 0 02 and 0 04 isodensity surfaces This data is written to the dumpfile on section 172 and 175 e generate potential derived charges by fitting to the potential points from 2 The total charge is constrained to 0 0 In addition to the dumpfile sections for the potential data the following keywords may appear on the POTFIT directive e CHARGE charge constrain charge e SYMMETRY constrain symmetry equivalent atoms to have the same charge e DIPOLE dx dy dz constrain dipole atomic units e CUTOFF scale exclude points closer than scale the covalent radius from a nucleus 8 Mulliken Analysis The purpose of this module is to provide for an increased level of analysis of a given set of molecular orbitals The default SCF options will typically provide a population analysis of the total SCF wavefunction In some instances it is useful to probe the individual molecular orbitals extracting quantities such as
23. ITLE Specify a title for the data array TITLE title css 6 14 Data Calculation TYPE TYPE keyword Specify the property to be calculated Valid keywords are given in Table 2 A more detailed description of the functions available is given below together with information regarding any other input data required Electron Density Functions In depicting the spatial characteristics of the density associated with one or more molecular orbitals the program computes densities according to the formula p r a OCC 0 r 1 where O denotes the i th molecular orbital and OCC its occupation number Plots of the amplitude of a single orbital i a r OCC O r 2 6 GRAPHICAL ANALYSIS 15 may also be generated Density Difference Function The atomic density difference function is defined as Atoms Apr pmalr gt gt pit 3 J The first term is the total electron density associated with a molecule The second term represents the sum of the electron densities of the atoms which constitute the molecule these being placed at the same positions they occupy in the molecule but which are assumed to have undergone no interactions with each other and have remained undistorted as in the free state The atomic density difference function provides an indication of the overall rearrangement of density which occurs when the atoms come together upon molecular formation The program incorporates an atomic SCF module so that c
24. LEV directive serves to specify the number of elements of the triangulated surface defining the dielectric boundary This directive is active when the SURFACE keyword is either SPHERE or JUFFER The directive is read to the variables TEXT BEMLEV using format A 13 DRF DIRECTIVES 49 1 TEXT should be set to the character string BEMLEV 2 BEMLEV is the level of detail of the triangulated sphere Valid options are a O results in 60 boundary elements b 1 results in 240 boundary elements c 2 results in 960 boundary elements The default is BEMLEV 0 13 194 JUFFER The JUFFER directive serves to specify the generation of a Juffer triangulated surface enveloping QM and classical if present atoms The directive consists of a single data line starting with JUFFER which may contain a number of keywords followed by their values The JUFFER keywords are 1 CYLWDTH width of a cylinder around a spoke The atom within this cylinder which is furthest away from the centre of the molecular system defines the position of the surface element associated with the spoke If CYLWDTH is not set or lt 0 0 it defaults to 2 maxrad BEMLEV 2 1 RPROBE where maxrad is the largest atomic radius of the QM and classical systems 2 SURFDIST distance of the surface defining point to the atom generating the surface If SURFDIST is not set or lt 0 0 it defaults to maxrad RPROBE where maxrad is the largest atomic radius of the QM and c
25. N 1 1 Introduction In the first part of this chapter we provide a description of the analysis options and associated data input available within GAMESS UK including i the calculation of 1 electron properties and localised molecular orbitals ii the graphical analysis of wavefunctions by the calculation of charge densities molecular orbitals atom difference densities and electrostatic potentials on a grid of points iii the calculation of potential derived charges with electrostatic potential data calculated using the graphics module to generate least squares fitted point charges at the nuclei and iv performing both Mulliken and Distributed Multipole Analyses We then describe the capabilities and data input associated with the Direct Reaction Field DRF model for solvation This model developed at the University of Groningen 1 2 is an embedding technique enabling the computation of the interaction between a quantum mechanically described molecule and its classically described surroundings 2 Analysis Modules Introduction The analysis modules of GAMESS UK are requested under control of the RUNTYPE ANALYSE directive Note that at present only one mode of analysis may be carried out in a given step when it is assumed that the vectors to be analysed are resident in the section nominated on the VECTORS directive The following points on eigenvector specification should be noted e While the SCF modules now support default eigen
26. NGRNAM1 characters are considered when deciding the exclusion of interactions 13 DRF DIRECTIVES 44 ii to define for which polarizabilities grouping to form a group polarizability should be attempted The NGRNAM2 characters of the group name following the NGRNAM1 characters are considered when deciding whether to attempt grouping the pre ceding atom polarizabilities iii label the classical atoms NOTE NGRNAM1 and NGRNAM2 may be specified on the GROUPING directive see above NOTE The names of the classical atoms are stored in a 16 character string the group name starting at character 7 There are thus a maximum of 10 characters available for the group name and NGRNAM1 may not exceed 8 to leave at least 2 characters for the grouping name NOTE A group is formed on the basis of the group name if the relevant part of the group name changes from one atom to the next and formation of group polarizabilities is requested see the GROUPING directive NOTE The specification of a group name is mandatory If no use is to be made for grouping purposes the best way to ensure independent treatment of the atoms is by using the group name to label the atoms uniquely NOTE When grouping under the GROUPING directive a change in group name at the NGRNAM2 characters governing grouping will signify the attempt to group the preceding atoms If further down the list the same group name for grouping is used again the first set of atoms will not be
27. RB SPIN 11 ANNIHILATE ENTER Note again that the NOs of the UHF and AUHF wave function are in fact identical the only difference lying in the occupation numbers 4 3 MP2 Calculations Now let us consider the date requirements when computing properties at the optimum geometry derived from an MP2 calculation TITLE H2C0 X1A1 MP2 DZ BASIS PROPERTIES ZMATRIX ANGSTROM C D 1 CO H 1 CH 2 HCO H 1 CH 2 HCO 3 180 0 VARIABLES CO 1 203 CH 1 099 HCO 121 8 END BASIS DZ RUNTYPE OPTIMISE PROPERTY ATOMS SCFTYPE MP2 NATORB 20 ENTER Having generated the MP2 optimised geometry the spinfree natural orbitals will be routed to section 20 on the Dumpfile and used in the subsequent properties calculation 4 SIMPLIFIED PROPERTY SPECIFICATION 6 4 4 CI Calculations Computing the default set of one electron properties at completion of Cl processing may be readily accomplished through the addition of the PROPERTY ATOMS data line Note that any such calculation requires the NATORB directive to specify the routing of the spinfree and where relevant the spin NOS to specified sections on the Dumpfile Note also that property evaluation under PROPERTY ATOMS control is only available for Direct Cl calculations and not Full Cl or coupled cluster calculations TITLE H2CO 3 21G CISD DCI PROPERTIES CALCULATION SUPER OFF NOSYM ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END RUNTYPE CI
28. RECTIVES 5l 13 19 8 DIELOUT The DIELOUT directive serves to specify the level of output associated with the surface defining the dielectric boundary The directive is read to the variables TEXT OUTDIEL using format 2A 1 TEXT should be set to the character string DIELOUT 2 OUTDIEL is the level of output requested The actual output depends on the type of surface requested Valid options are a STANDARD Standard output b SOME c MODERATE d EXTENDED e ALL Maximum output The default is DIELOUT STANDARD 13 19 9 EPSSTAT The EPSSTAT directive serves to specify the static dielectric constant associated with the di electric continuum DIELTYP STAT The directive is read to the variables TEXT EPS1 using format A F 1 TEXT should be set to the character string EPSSTAT 2 EPS1 is the static dielectric constant This should be a number larger than 1 0 to take effect Values smaller than 1 0 are ignored a value of 1 0 effectively means the dielectric is a vacuum and is therefore not active A finite ionic strength see subdirective KAPPAS may still be specified though The default is EPSSTAT 1 0 13 19 10 EPSOPT The EPSOPT directive serves to specify the optic dielectric constant associated with the dielectric continuum DIELTYP OPT The directive is read to the variables TEXT EPS2 using format A F 1 TEXT should be set to the character string EPSOPT 2 EPS2 is the optic dielectric constant
29. This should be a number larger than 1 0 to take effect Values smaller than 1 0 are ignored a value of 1 0 effectively means the dielectric is a vacuum and is therefore not active A finite ionic strength see subdirective KAPPAO may still be specified though The default is EPSOPT 1 0 13 DRF DIRECTIVES 52 13 19 11 KAPPAS The KAPPAS directive serves to specify the ionic strength associated with the static dielectric constant associated with the dielectric continuum DIELTYP STAT The directive is read to the variables TEXT KAPPAS using format A F 1 TEXT should be set to the character string KAPPAS 2 KAPPAS is the ionic strength associated with the static dielectric constant This should be a number larger than 0 0 to take effect Values smaller than 0 0 are ignored The default is KAPPAS 0 0 13 19 12 KAPPAO The KAPPAO directive serves to specify the ionic strength associated with the optic dielectric constant associated with the dielectric continuum DIELTYP OPT The directive is read to the variables TEXT KAPPAO using format A F 1 TEXT should be set to the character string KAPPAO 2 KAPPAO is the ionic strength associated with the optic dielectric constant This should be a number larger than 0 0 to take effect Values smaller than 0 0 are ignored The default is KAPPAO 0 0 13 20 CLASCLAS The CLASCLAS directive serves to specify the types of interaction between classical subsystems to be calculated The
30. YSIS 20 6 17 Data Calculation SFAC The SFAC directive specifies a constant that will be used to multiply all calculated grid data values The default scale factor is 1 0 except for electrostatic potential plots in which case it is 627 707 to convert the values to kcal mol 6 18 Data Calculation RADII The RADII directive allows the user to input a set of radius values for use in the van der Waals function calculation see above it is followed by a series of records each specifying an atom label and the radius for all atoms with that label The input is terminated with a record containing the string END By default radii are expected in atomic units angstroms may be used if the string ANGS is added on the RADII directive 6 19 Data Calculation SECTION Specify a section number isect on the dumpfile where the calculated data is to be stored SECTION isect Storage of the data is required is required in the following circumstances e the grid is to be written to the punchfile e the data is on a 3D regular grid and is to be used in a contour grid generation step 6 20 Data Calculation RESTORE The RESTORE Directive is used to bring a grid or data from a dumpfile into memory The data must have been written by a SECTION directive see above and the first keyword on the directive DATA or GRID is used to specify the whether a grid definition or data is required It is an error to specify DATA if the dumpfile section actu
31. a which will appear as peaks on the projected plot and thus to determine VMAX the value of the greatest maximum lt SCAMAX In the event that no such maximum is detected VMAX will be set to SCAMAX All maxima with a greater value than VMAX FACTOR will appear as beheaded peaks on the final plot e SCAMIN FACTOR the grid of values is scanned to detect all local minima which will appear as troughs on the projected plot and thus to determine VMIN the value of the lowest minimum gt SCAMIN In the event that no such minimum is detected VMIN will be set to SCAMIN All minima with a value less than VMIN FACTOR will appear as beheaded troughs on the final plot The projected plot will be normalized to VMAX FACTOR VMIN FACTOR If the SCALE directive is omitted SCAMAX is set to 0 7 SCAMIN to 0 7 and FACTOR to 1 2 6 29 Termination of GRAPHICS Input Data input for Graphical Analysis is terminated by presenting a valid Class 2 directive This might typically be the VECTORS directive instructing the analysis module as to the source of eigenvectors to be analysed 7 Potential Derived Charges The potential derived charges module uses electrostatic potential data calculated using the graphics module to generate least squares fitted point charges at the nuclei The module is invoked by the POTFIT directive under control of RUNTYPE ANALYSE An example of the input data is given below TITLE PDC CALCULATION ZMAT ANGS 0 H 11 0
32. alculations on the ground states of the component atoms are performed in line with the basis set of each atom the same as that used in the parent molecule These plots are known as atomic difference plots the program is capable of generating such plots of molecular systems with component atoms up to and including zinc A more general form of the density difference function the molecular density difference Ap r gt pilr Dpj r 4 a J is used in the construction of molecular difference plots which allows the user to display the density resulting from the addition or subtraction of up to 15 component density functions Two examples of the value of such plots are e Illustrating the effect on a molecular charge distribution resulting from an extension of the basis set so that a typical plot would be constructed using the function Ap r E y 5 e In depicting the rearrangement of electron density which occurs when the component ligands and metal atom of a transition metal complex come together to form the molecular system so that for a complex MX the following difference function Ap r Peompler r pm r gt pxi r 6 would be constructed this being the molecular analogue of the atomic density difference function 6 GRAPHICAL ANALYSIS 16 Electrostatic Potential Function The value of the electrostatic potential created by the electronic distribution and nuclear charge of a molecule in the differen
33. ally contains a grid definition and vice versa The remaining data items are the Ifn eg ED3 for the current dumpfile iblk is the starting block of the dumpfile usually 1 and isec the dumpfile section as specified on the SECTION directive RESTORE GRID DATA lfn iblk isec 6 21 Data Calculation SURF The SURF directive is used to generate one or more isovalue surfaces from a 3D dataset and calculate data at points on that surface It is presented after directives requesting the calculation of the 3D dataset The syntax of the surf directive is as follows 6 GRAPHICAL ANALYSIS 21 SURF type isec imo leveli level2 where e type is the property to be calculated lt may be one of the valid keywords of the calcu lation TYPE subdirective given in Table 2 and may be followed by an MO index where appropriate e isec is the a section number on the current dumpfile for output of the first grids generated Subsequent data and grids will be saved to consecutive section numbers e levell level2 are a series of values at which the isovalue surface is to be generated The result is the same as if the user had made a series of grid definition requests of type CONTOUR and data calculation requests For each level requested GAMESS UK will generate a surface grid and write it to the dumpfile If the 3D data being contoured is of type MO or DENS the gradient of the field at every point will be calculated and stored The requeste
34. centre The default is that all sites have relative radius 1 0 9 DISTRIBUTED MULTIPOLE ANALYSIS 29 9 4 LIMIT LIMIT name lmax Limit the rank of multipoles on sites with the name given to Imax at most Contributions with higher ranks are moved to other sites If no name is given the limit applies all sites default and maximum is 20 for the linear version 10 otherwise 9 5 SHIFT SHIFT tshift Distribute multipoles from an overlap contribution around several dma sites using a Gaussian weighting function tshift is a cutoff parameter maximum 1 minimum le 6 A value of 1 0 the default means distribution is to the nearest site only 9 6 LINEAR This directive invokes a faster version of the DMA program which is applicable when all the atoms lie in a line parallel to the z axis and only the z components of the multipoles are required In this case the maximum rank is 20 The option is revoked if the molecule is found not to be linear If the molecule is subject to an external field or is not in a singlet sigma state there may be other non vanishing multipole moments which will not be calculated however the ql0 will still be correct 9 7 GAUGE GAUGE ox oy oz The GAUGE directive resets the coordinate origin and is followed by the coordinates of the new origin The distributed multipole analysis is not affected but the total multipoles are referred to the new origin The sites as printed out and in the punchfile are specif
35. d property will then be calculated for every point When more than one level is required it is necessary to restore the 3D dataset prior to each contouring operation This is performed automatically by the program but a consequence of this that the 3D data must be stored on the dumpfile is the responsibility of the user The user should note that there is a limit noted above to the number of of grid definitions data calculations etc which may be requested for each invocation of RUNTYPE ANALYSE and the totals include requests generated implicitly by SURFACE All grid definitions and data arrays are written to the dumpfile with section numbers counting from the isec value given in the order in which they are generated The user is responsible for ensuring that any data required by other software is written to the punchfile The grid definitions will be appear in the punchfile as part of the property but not gradient datasets and are not requested explicitly The form of the punch directive required should be clear form the examples below 6 21 1 Example Potential on an isodensity grid The following GAMESS UK input assumes that a job to calculate the closed shell SCF wave function has already been completed RESTART NEW PUNCH GRID 161 162 164 165 TITLE FORMALDEHYDE SURFACE ZMAT ANGS Cc 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END BASIS DZ 6 GRAPHICAL ANALYSIS 22 RUNTYPE ANALYSE GRAPHICS GDEF TITLE 3D
36. dielectric constants may be given on input If the Direct Reaction Field is active only the optic component of the dielectric response is coupled directly to the charge distribution for calculation of the estimate of the dispersion interaction since this part reflects the electronic part of the dielectric response the static component is coupled through the Average Reaction Field The properties of the dielectric continuum enveloping the molecular system that may be specified are both the dielectric constant and the ionic strength This is due to the implementation of the Poisson Boltzmann equation solver on the boundary surface rather than just the Poisson equation solver This option may be useful for studying solvation effects in ionic solutions NOTE At present the analytical gradients both on the QM system and on the classical points charge and or polarizabilities are not available limiting geometry optimization capabilities of this module 13 DRF Directives The Direct Reaction Field model is invoked through specifying a block of data marked by the single line directives REACT at the start and END at the end Inside this block the positions and magnitude of the point charges and polarizabilities the definition of an enveloping surface to mark the beginning of a dielectric and all DRF options may be specified by their respective directives given below The definition of the QM system remains to be specified through the ZMATRIX dir
37. e are the homogeneous conical and the exponentially decreasing spherical shapes 12 2 Damping Functions Problems with numerical stability and or unphysical behaviour may arise when using the full Coulomb potentials and fields for the calculation of interactions between subsystems that are nearby Use of full Coulomb potentials does not account for any overlap of the charge clouds that would damp the potential if both subsystems were treated quantum chemically Thole developed damping functions to account for overlap effects and they may be used to damp the potentials and fields between QM system and classical systems and between classical subsystems 8 Two types of damping function are available 1 damping based on the assumption that the charge is distributed homogeneously in a cone of certain width around the nucleus expansion centre 2 damping based on the assumption that the charge is exponentially decreasing radially from the nucleus expansion centre Both models have been used to construct molecular polarizabilities from atomic polarizabilities 8 123 CHARMM Model Repulsion The repulsion between atoms in the QM system and classical system and between the atoms in the classical subsystems is treated by using the CHARMM force field expression 6 E ES 3 aia ritr y 2 rep CHARMM Dic 4 as mi y 05 m ij where a is the polarizability of atom i r is the radius of atom 2 and n is the number of valence electrons of atom i and
38. e default is QMRADI TABLE NOTE The radius is calculated as r fsnapea with fshape equal AFCT specified in subdi rective DAMPING 13 17 CLASRADI The CLASRADI directive specifies the method for calculating the radii of atoms in the classical partition for use in both construction of a boundary surface marking the dielectric and the CHARMM QM classical repulsion if appropriate The directive consists of a single data line read to the variables TEXT RADOPT using format 2A 1 TEXT should be set to the character string CLASRADI 2 RADOPT is the option for selecting the radii Valid options are a TABLE look up from internal table Bondi s van der Waals radii b CONEPOL calculated from Thole s polarizability optimized for the damping according to a conical charge density 13 DRF DIRECTIVES 43 c EXPOPOL calculated from Thole s polarizability optimized for the damping according to a exponential charge density d USERPOL calculated from assigned polarizability whether given on input see EXTERNAL subdirective or through look up The default is CLASRADI TABLE NOTE The radius is calculated as r fsrapea with fshape equal AFCT specified in subdi rective DAMPING NOTE This directive must proceed the EXTERNAL directive to be effective 13 18 EXTERNAL The EXTERNAL directive marks the beginning of the block input for x y z coordinates charge polarizability and radius of the atoms in the classically t
39. e is followed by ncards data records containing the x y and z coordinates of a data point in a u in the coordinate system of the molecule after reorientation by the GAMESS UK symmetry analysis routines 6 5 4 TYPE CONTOUR value Generate points on an isovalue surface The section number or calc id refers to an array of data values calculated on a regular 3D grid which are to be contoured 6 5 5 TYPE WRAP value Points are generated on an isodensity surface without storage of a 3D array of density points If this option is used it must follow the specification of a regular 3D grid which defines the volume and mesh density for the contouring 6 6 Grid Definition ORIG The ORIG directive specifies the origin ie centre of the grid it applies only to the grid types 2D 3D and SPHERE ORIG x y z 6 GRAPHICAL ANALYSIS 13 6 7 Grid Definition X and Y Set the direction of the plot axes for 2D and 3D grid types By default the first plot axis referred to as X lies along the x direction of the molecular coordinate system and the second along y X XX Xy XZ Y yx yy yz 6 8 Grid Definition SIZE Set the grid size edge length for 2D and 3D grids or the radius for spherical grids If only one value is specified it will be used for all dimensions but extra values may be provided to set the y and for 3D z axis lengths independently SIZE sx lt sy lt sz gt gt 6 9 Grid Definition POINTS Set the mesh density
40. e nuclear attraction energy interaction of all nuclei with the RF induced by all electrons plus interaction of all electrons with the RF induced by all nuclei screening of the two electron energy interaction of all electrons with the RF induced by all electrons screening of the electronic self energy sum of interaction of each electron with the RF induced by itself only with the DIRECT RF option see also the GAMDRF directive molecular reaction field stabilisation interaction of the QM system with the RF induced by the QM system equilibrium molecular polarisation energy energy cost to induce dipole moments and surface polarisation by the QM system 2 energies associated with the classical system collected per analysis group vacuum classical electrostatic interaction interaction between point charges in the classical sub system s vacuum dispersion energy estimate polarizability based dispersion interaction be tween atoms in the classical sub system s see also CLASDISP directive vacuum repulsion energy estimate CHARMM repulsion interaction between atoms in the classical sub system s see also the HBOND directive vacuum classical interaction energy sum of the first three contributions screening of classical electrostatic energy interaction of all charges in analysis group A with the RF induced by all charges in analysis group B and vice versa equilibrium classical polarisation energy energy cost to induce
41. e same second part of the group name will result in two rather than one group polarizabilities from those atoms The ANAL n where n is an integer maximum 10 is an optional addition to the forced grouping causing analysis of the RF contributions to the total energy to be split into groups n provides an index into the analysis groups In this way contributions from e g first and second solvent shells or from different residues in a protein may be separated EXAMPLE 2 classical water molecules Here are a numer of examples of 2 classical water molecules 1 EXTERNAL part of input external o wi 0 796 3 459378 4 492394 0 0 h wi 0 398 3 459378 5 595494 1 4325 h wi 0 398 3 459378 5 595494 1 4325 group anal 1 o w2 0 796 3 459378 4 492394 0 0 8 4 3 1 h w2 0 398 3 459378 5 595494 1 4325 3 2 2 5 h w2 0 398 3 459378 5 595494 1 4325 3 2 2 5 group anal 2 end With all other directives at their default values the following attributes are given to the classical system copied from output induced dipole criterion for grouping not met WARNING grouping forced by user but grouping criteria not met grouping information may be obtained by specifying the REACT subdirective DRFOUT MORE 6 points found on input of which 6 polarisable constructed 8 charged points O point polarisabilities and 2 group polarisabilities classical system specification name x y z charge radius alfa b 3 effalf b 3 analysis group wigr 3 459378
42. ected The default is AGRPM 0 01 in au NOTE This directive must proceed the EXTERNAL directive to be effective 13 13 AGRPC The AGRPC directive specifies the cosine criterion for constructing group polarizabilities from atomic polarizabilities under the control of the GROUPING directive The directive consists of a single data line read to the variables TEXT AGRPC using format A F 1 TEXT should be set to the character string AGRPC 2 AGRPC is the minimum allowed cosine of the angle between the induced dipole moments due a unit charge at the nearest QM atom as calculated with and without the grouping If the cosine is smaller grouping is not effected 13 DRF DIRECTIVES 41 The default is AGRPC 0 99 NOTE This directive must proceed the EXTERNAL directive to be effective 13 14 DAMPING The DAMPING directive serves to specify the type of damping function and corresponding width parameter to be used to damp electrostatic fields by to avoid the so called polarization catas trophe see section 12 2 It also controls the selection of default atom polarizabilities The directive consists of a single data line starting with DAMPING which may contain a number of keywords AFCT followed by its value The DAMPING keywords are 1 OFF to specify use of the full Coulomb operator 2 EXPO to specify the damping associated with an exponentially decreasing spherical shape function 3 CONE to specify the damping associated with a unif
43. ective Any capping atoms to be introduced when excising a QM system from a covalently bonded superstructure must be specified with the QM system since there is no automatic generation for these atoms Also the user is responsible for avoiding close contacts between QM capping atoms and classical atoms The REACT subdirectives are given below 13 DRF DIRECTIVES 36 13 1 FIELD The FIELD directive specifies the level of coupling between QM system and surroundings The directive consists of a single data line starting with FIELD which may contain a number of keywords followed by their values The FIELD keywords are 1 STAT specifies presence of static embedding potential followed by the desired level 2 REAC specifies presence of response embedding potential followed by the desired level The level of embedding may be a NONE this embedding is not taken into account b PERT this embedding is added as a perturbation after convergence of the wave function c SCF this embedding is treated self consistently with the wave function The default is FIELD STAT NONE REAC NONE 13 2 DRFOUT The DRFOUT directive serves to specify the level of output for the DRF extension The directive consists of a single data line read to the variables TEXT OUTOPT using format 2A 1 TEXT should be set to the character string DRFOUT 2 OUTOPT is the level of output for the DRF module Valid options are a STANDARD b SOME Information
44. ed The default is GAMDRF 0 0 13 5 INCLPOL The INCLPOL directive serves to specify the strength of the reaction field coupled to the QM system The reaction field may either be coupled back in full or at half strength only in which case the polarization energy is taken into account beforehand The directive is read to the variables TEXT OPTION using format 2A 1 TEXT should be set to the character string INCLPOL 2 OPTION may be either ON or OFF When INCLPOL ON the polarization is taken into account beforehand The default is INCLPOL ON 13 6 EXPANDCM The EXPANDCM directive specifies the use of the centre of nuclear charge of the QM partition as an extra expansion centre for the D RF integrals The directive consists of a single data line read to the variables TEXT EXPOPT using format 2A 1 TEXT should be set to the character string EXPANDCM 2 EXPOPT can be set to the character strings ON or OFF The default is EXPANDCM OFF 13 DRF DIRECTIVES 38 13 7 ASSIGN The ASSIGN directive specifies the way the overlap distributions are assigned to the expansion centres The centre of a charge distribution is defined by 2 7 7 i 7 The directive consists of a single data line read to the variables TEXT ASGNOPT using format 2A 1 TEXT should be set to the character string ASSIGN 2 ASGNOPT can be set to the following character strings a DISTANCE assign overlap distributions on the basis of distance of the c
45. entre of the overlap distribution to the expansion centres The overlap distribution is assigned to the nearest expansion centre If two or more centres are equally close the assignment is arbitrarily to the last centre encountered in the search b OLAPTOCM assign all two centre overlap distributions to the expansion centre at centre of nuclear charge only with EXPANDCM ON c EQUATOCM assign overlap distributions that are equally close to one or more expan sion centres to the expansion centre at centre of nuclear charge only with EXPANDCM ON d MIDPTS add midpoints between atoms as expansion centres and assign as with DISTANCE e ALLDISTR expand each overlap distribution around its own centre If any expansion centre is close to one already defined the expansion centre will be shared The default is ASSIGN DISTANCE NOTE Extra other expansion centres may be specified by using BQ centres in the ZMATRIX directive These centres will then be used as expansion centres Note that if the BQ centres carry charge interaction with the QM atoms will be included in the QM energy interaction with classical atoms in the QM classical interaction 13 8 GROUPING The GROUPING directive specifies the attempt to construct group polarizabilities from atomic polarizabilities on the basis of the atoms group name see the EXTERNAL directive It also serves to define the number of characters in the group name of atoms used to exclude interac
46. erturbation SOP expression for the dispersion between two fragments by inserting the resolution of the identity in the first term The k 0 terms in the first and second terms cancel and Edisp DRF 5 Reo O F t k a k F 0 This expression is the same as the SOP expression in the Unsold approximation but for a factor Us UA Us where Us and U4 are mean excitation energies for the polarizable and QM systems respectively This factor must be supplied by the user This factor may be estimated from e g onization energies experimental or calculated If S and A are identical the factor is 5 The user may specify this factor to switch on this interaction By default this factor is set to zero and therefore the QM system is embedded in the Average Reaction Field only The expressions above have been derived for a QM system interacting with one polarizability By substituting the effective response of coupled polarizabilities and dielectric response for a the estimate for the dispersion interaction with all the surroundings may be made The dispersion interaction between classically described molecules is given by the Slater Kirkwood expression Tr a T 2 0 E ee ijd disp clas 4 Vaifmi es mj where a is the polarizability of atom i n is the number of valence electrons of atom 2 and 75 is the dipole dipole interaction tensor between atoms 7 and j A minimum number of parameters is introduced if one uses the same polarizabilitie
47. g the data requirements when performing a UHF wavefunction The following data sequence would be required when evaluating the properties based on a direct UHF calculation with the alpha and beta UHF MOs routed to the default sections 2 and 3 of the Dumpfile in the absence of explicit section specification on the ENTER directive TITLE H2C0 3A2 UHF PROPERTIES 3 21G BASIS MULT 3 ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END SCFTYPE DIRECT UHF PROPERTY ATOMS ENTER The same calculation may be performed based on the spinfree and spin natural orbitals of the UHF wavefunction in this case the NATORB data lines will be used to route the spinfree and spin natural orbitals to sections 10 and 11 of the Dumpfile respectively and these orbitals will be used in computing the 1 electron properties thus TITLE H2C0 3A2 UHF NO BASED PROPERTIES 3 21G BASIS MULT 3 ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END SCFTYPE DIRECT UHF PROPERTY ATOMS NATORB 10 NATORB SPIN 11 ENTER 4 SIMPLIFIED PROPERTY SPECIFICATION The following data sequence would be required if the user wished to compute the properties of the annihilated UHF wavefunction TITLE H2CO 3A2 annihilated UHF properties 3 21G BASIS MULT 3 ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END SCFTYPE DIRECT UHF PROPERTY ATOMS NATORB 10 ANNIHILATE NATO
48. group name starting at character 7 There are thus a maximum of 10 characters available for the group name and NGRNAM1 may not exceed 8 to leave 2 characters for grouping polarizabilities NOTE This directive must proceed the EXTERNAL directive to be effective 13 9 DSTGRP The DSTGRP directive specifies the minimum distance criterion for constructing group polariz abilities from atomic polarizabilities under the control of the GROUPING directive The directive consists of a single data line read to the variables TEXT DSTGRP using format A F 1 TEXT should be set to the character string DSTGRP 2 DSTGRP is the minimum distance any classical atom in the prospective group must be separated from any QM atom for the grouping to be considered Grouping is not effected if any classical atom in the prospective group is closer to any QM atom than DSTGRP The default is DSTGRP 15 0 NOTE This directive must proceed the EXTERNAL directive to be effective 13 10 DSTMAX The DSTMAX directive specifies the maximum distance criterion for constructing group polariz abilities from atomic polarizabilities under the control of the GROUPING directive The directive consists of a single data line read to the variables TEXT DSTMAX using format A F 1 TEXT should be set to the character string DSTMAX 2 DSTMAX is the maximum distance the nearest classical atom in the prospective group should be from any QM atom to effect grouping If that atom is f
49. he reaction field due to induced dipoles at the polarizabilities and surface polarization at the dielectric boundary by including these fields in the one and two electron parts of hamiltonian and Fock matrix respectively For many systems the difference in total energy between the fourth and fifth levels is small the self consistent treatment of the electrostatic field is often found to change results substantially from a fully perturbative treatment The response of the surroundings is calculated through solving the set of linear equations that result from coupling the moments induced at the polarizabilities and at the boundary elements the latter resulting from the linearized Poisson Boltzmann equation This formally requires the inversion of what is called the relay matrix which contains all the couplings The procedure implemented here is the LU decomposition of the relay matrix The LU decomposition is the most expensive step in the embedding procedure Care should therefore be taken to limit the number of polarizabilities and boundary elements The relay matrix is square matrix of a maximum of 3 N oy Noe X 3 Npo Noe elements where No is the number of polarizabilities and Ny is the number of boundary elements In the case of specifying a non zero ionic strength of the dielectric another Nye is added to the dimensionality of the relay matrix 11 Total energy in the DRF model The total energy in the DRF model is may be partitio
50. his default evaluation may be conducted with basis sets comprising s p d and f basis functions We illustrate below a number of considerations that arise as a function of RUNTYPE and SCFTYPE processing when invoking this default property specification 4 1 SCF Calculations The following data sequence would be required to generate the default list of properties on completion of an SCF calculation of the formaldehyde molecule TITLE H2CO 3 21G BASIS SCF DEFAULT 1 E PROPERTIES ZMATRIX ANGSTROM C 0 1 1 203 H 1 1 099 2 121 8 H 1 1 099 2 121 8 3 180 0 END RUNTYPE SCF PROPERTY ATOMS ENTER 4 SIMPLIFIED PROPERTY SPECIFICATION 4 In this example the set of MOs to be used in the property evaluation will be retrieved from the default section of the Dumpfile written to by the closed shell SCF module i e section 1 4 2 UHF Calculations A somewhat different approach may be required when computing the one electron properties derived from a wavefunction with more than one set of MOs e g a UHF wavefunction or in cases where only the total density matrix and not an associated set of MOs is available e g in an MP2 calculation In both cases the user may need to ensure that the associated set of spinfree natural orbitals and where relevant SPIN natural orbitals are generated by specification of the NATORB directive s used to route the NOs to a nominated section on the Dumpfile We illustrate this effect by first considerin
51. ied b ORGPOL or EFFPOL to switch between the use of the input atom polarizabilities and the effective atom polarizabilities after group polarizability formation This option affects atom polarizabilities only 13 DRF DIRECTIVES 42 c ISODIS or NONISO to switch between the use of isotropic and anisotropic polarizabil ities Atom polarizabilities that have not been used in the construction of any group polarizability are always isotropic and this option does not affect the dispersion interaction between such atoms The default is CLASDISP ATOMPOL ORGPOL ISODIS NOTE This directive must proceed the EXTERNAL directive to be effective in setting the correct polarizabilities 13 16 QMRADI The QMRADI directive specifies the method for calculating the radii of atoms in the QM partition for use in both construction of a boundary surface marking the dielectric and the CHARMM QM classical repulsion if appropriate The directive consists of a single data line read to the variables TEXT RADOPT using format 2A 1 TEXT should be set to the character string QMRADI 2 RADOPT is the option for selecting the radii Valid options are a TABLE look up from internal table Bondi s van der Waals radii b CONEPOL calculated from Thole s polarizability optimized for the damping according to a conical charge density c EXPOPOL calculated from T hole s polarizability optimized for the damping according to a exponential charge density Th
52. ied with respect to the new origin 98 NONUCLEAR The nuclear contribution to the multipoles is not evaluated 10 THE DRF MODEL FOR SOLVATION 30 10 The DRF Model for Solvation The Direct Reaction Field model for solvation developed at the University of Groningen 1 2 is an embedding technique enabling the computation of the interaction between a quantum mechanically described molecule and its classically described surroundings The classical sur roundings may be modelled in the following ways 1 by point charges to model the electrostatic field due to the surroundings 2 by polarizabilities to model the electronic response of the surroundings 3 by an enveloping dielectric to model bulk response both static and electronic of the surroundings 4 by an enveloping ionic solution characterized by its Debye screening length The four representations may be combined freely to model all aspects of the surroundings The best results with this model for solvation studies have been obtained by immersing the QM solute by 2 3 layers of explicitly described point charges and polarizabilities solvent molecules enveloped by a surface defining the boundary between the microscopic system and a dielectric with bulk solvent properties dielectric constant 2 The model has also been applied to active sites in proteins 6 Special care has to be taken to avoid spurious electrostatic and reaction field interactions with nearby atoms when bond
53. in each SCF cycle b DISK 2 electron RF integrals are added to the vacuum 2 electron integrals stored on disk The default is DRFTWOEL DIRECT NOTE This keyword only takes effect when the QM density is treated self consistently with the reaction field NOTE DRFTWOEL DISK is currently valid only in the following combination SUPER OFF NOSYM and GAMDRF 1 0 14 DRF Output Analysis of D RF Energies The D RF module produces additional output at the end of the normal output This is a full analysis of the D RF contributions to the energy The output is structured as follows 1 energies associated with the quantum system T electron kinetic energy operator Vo vacuum one electron energy operator go vacuum two electron energy operator vacuum nuclear repulsion one electron energy expectation value of T Vo using the final density a b c electron kinetic energy expectation value of T using the final density d nuclear attraction energy expectation value of Vo using the final density e two electron energy expectation value of go using the final density 14 DRF OUTPUT ANALYSIS OF D RF ENERGIES 54 f scf energy converged total energy of the QM system This may include contributions from static and reaction fields if the QM density is treated self consistently with these fields screening of the nuclear repulsion energy interaction of all nuclei with the RF induced by all nuclei screening of th
54. is groups estimate of the dispersion energy the DRF estimate for QM classical dispersion only in the Direct RF option see section 12 4 and the GAMDRF directive 5 summary of the contributions a b total energy of quantum system expectation value of the vacuum hamiltonian in cluding nuclear repulsion with the final density total energy of classical system quant mech classical interaction energy total interaction energy of QM system with surroundings equilibrium polarisation energy total cost for inducing dipole moments and surface polarization configuration total energy energy of the QM classical system as a whole REFERENCES 56 References 1 A H de Vries P Th van Duijnen A H Juffer J A C Rullmann J P Dijkman H Merenga and B T Thole J Comp Chem 16 1995 37 55 doi 10 1002 jcc 540160105 erratum 1445 1446 doi 10 1002 jcc 540161113 2 P Th van Duijnen and A H de Vries Int J Quant Chem 60 1996 1111 doi 10 1002 SICI 1097 461X 1996 60 6 1111 AID QUA2 3 0 C0 2 2 3 JM Foster and S F Boys Rev Mod Phys 32 1960 300 doi 10 1103 RevModPhys 32 300 4 J Pipek and P G Mezey J Chem Phys 90 1989 4916 doi 10 1063 1 456588 5 A J Stone Chem Phys Lett 83 1983 233 doi 10 1016 0009 2614 81 85452 8 6 J P Dijkman and P Th van Duijnen Int J Quant Chem Quant Biol Symp 18 1991 49 doi 10 1002 qua 560400710 7 B R Brooks R E Bruccoleri
55. just the set of valence molecular orbitals omitting all core or bitals from the process The presence of the DEFAULT data character string signals the termination of LOCAL input An alternative to utilising the DEFAULT option above is to include additional data lines that explicitly nominate the molecular orbitals to be incorporated Such data lines are read to an array LMO I I 1 NACT using free l format When specifying such an orbital set the last data field presented should be the character string END Example 1 The single data line LOCAL OVERLAP 1234567 8 9 END requests use of the overlap based localisation technique due to Pipek and Mezey with molecular orbitals 1 9 to be included Example 2 The single data line LOCAL OVERLAP DEFAULT 5 LOCALISED MOLECULAR ORBITALS 9 requests use of the overlap based localisation technique due to Pipek and Mezey with only the set of valence molecular orbitals to be included Example 3 LOCAL 2345679 END Declares molecular orbitals 2 to 7 inclusive plus molecular orbital 9 to be active in the Foster Boys localisation process Example 4 LOCAL 234567 9 END This sequence has an equivalent effect to that of Example 3 Example 5 LOCAL 2 TO 7 9 END The above sequence shows an abbreviated form of specifying the list of molecular orbitals in voking the character string TO to link together a sequence of consecutive numbered active molecular orbitals This sequence
56. lassical systems The default is JUFFER CYLWDTH 1 0 SURFDIST 1 0 NOTE RPROBE may be defined in subdirective CONNOLLY 13 195 CONNOLLY The CONNOLLY directive serves to specify the generation of a Connolly surface enveloping QM and classical if present atoms The directive consists of a single data line starting with CONNOLLY which may contain a number of keywords followed by their values The CONNOLLY keywords are 1 MXSURPTS maximum number of surface elements to be generated by the Connolly algo rithm The algorithm is satisfied if the number of surface points is between MNSURPTS and MXSURPTS 2 MNSURPTS minimum number of surface elements to be generated by the Connolly algo rithm If unspecified it is set equal O 8 MXSURPTS 13 DRF DIRECTIVES 50 3 SPDENS Connolly surface point density Because the surface point density is optimized when setting MXSURPTS specification of both MXSURPTS and SPDENS conflicts and results in an error message 4 RPROBE probe radius for defining solvent accessible surface RPROBE 0 0 yields the Van der Waals surface The default is CONNOLLY MXSURPTS 200 RPROBE 1 0 NOTE Care is required when specifying SPDENS the number of surface points generated is unchecked and a large relay matrix to be LU decomposed may result NOTE RPROBE may also be relevant with SURFACE JUFFER 13 196 SOLVENT The SOLVENT directive serves to specify the solvent name associated with the dielectric con tin
57. lid a SPHERE The surface is a triangulated sphere around 0 0 0 The radius and the number of surface points may be further specified by the DIELECTRIC subdirectives SRADIUS and BEMLEV respectively b JUFFER The surface is generated by Juffer s method which distorts a triangulated sphere to envelop the atoms according to the molecular shape The surface is constructed by searching for the atom furthest away from the centre of the initial sphere along a number of spokes Each spoke defines a cylinder within which an atom is to be found If no atom is found within the cylinder the program terminates The number of surface points may be further specified by the DIELECTRIC subdirective BEMLEV and the location of the surface w r t the atom positions by the subdirectives JUFFER and CONNOLLY c CONNOLLY The surface is generated by using M L Connolly s surface program MSCON 11 which has been made part of GAMESS UK Further specification of the Connolly surface may be given through the CONNOLLY directive The default is SURFACE SPHERE 13 19 2 SRADIUS The SRADIUS directive serves to specify the radius of a triangulated sphere around 0 0 0 defining the dielectric boundary with SURFACE SPHERE The directive is read to the variables TEXT SPHERAD using format A F 1 TEXT should be set to the character string SRADIUS 2 SRADIUS is the radius of the triangulated sphere The default is SRADIUS 1000 0 13 193 BEMLEV The BEM
58. lid Class 2 directive 6 4 Grid Definition TITLE Provide a title for the grid TITLE title string 6 5 Grid Definition TYPE The type of grid is specified by the TYPE directive TYPE is followed by a keyword specifying the type of grid to be generated and other data as required by the grid type Valid keywords are given in Table 1 The individual grid generation modes are described below 6 GRAPHICAL ANALYSIS 12 6 5 1 TYPE 2D or TYPE 3D Generate regular 2 or 3D grids The origin centre of the grid is set using the ORIG directive and the X and Y directives set the orientation The number of points is set with the POINTS directive and the edge lengths using SIZE see below 6 5 2 TYPE SPHERE Generate a grid of points on the surface of a sphere of given radius The centre default 0 0 0 0 0 0 can be set using the ORIG directive The number of points is set with the POINTS directive The radius is set using the SIZE directive The SPHERE directive may optionally be followed by one of the keywords RAND or SYMM RAND which is the default requests that random starting latitude values be used for each ring of points at a given longitude SYMM requests that the generated grid preserve axial rotation symmetry and must be followed by an integer specifying the order of rotation symmetry required 6 5 3 TYPE CARDS ncards Read a set of points from the input file The number points ncards must be specified The directiv
59. must be noted 6 GRAPHICAL ANALYSIS 18 e Any orbital omitted from the list specified on the occupation definition lines will be assigned zero occupancy and thus will make no contribution to the grid of function values to be constructed e It is envisaged that the OCCDEF directive will not be required when generating grids of total electron density atomic density difference and interaction potentials In these three cases the occupation numbers should reflect the overall orbital occupancy in the molecule and should be just the values calculated during the construction of the molecular orbitals and output to the Dumpfile e The OCCDEF directive should be used when analysis of the electron density associated with a certain subset of orbitals is required Example OCCDEF 2 0 1 TO 5 7 END The grid of values will be generated assuming the first five molecular orbitals together with orbital 7 are doubly occupied All other orbitals will be assigned zero occupancy 6 16 Data Calculation CONFIG The CONFIG directive is only applicable when generating a grid of atomic density difference and may be used to specify the configuration to be used in computing the atomic density dis tribution corresponding to the ground state of the atoms In the absence of this directive spherically symmetric atoms are chosen with equal occupation of the degenerate open shell orbitals The user should note that applying a CONFIG specification will n
60. ned in various contributions 1 energy of the quantum system This is the energy of the quantum mechanical system as calculated with the supported wave functions Any change in energy upon interaction with the classical system is to be measured against a vacuum calculation on the quantum mechanical system 2 energy of the classical system This is the energy of the classical system calculated as if there were no QM system present The zero of energy depends on the specification of the classical system for example atoms may be defined to be part of molecules excluding their interactions making the infinitely separate molecules defining the zero of energy rather than infinitely separate atoms In this energy interactions between classical subsystems e g molecules are included They may be electrostatic dispersion repulsion and induction interactions 3 interaction energy This is the sum of all separable interaction energies a electrostatic interactions interactions between point charges in the classical system and the QM charge distribution nuclei and electrons 12 FEATURES OF THE DRF MODEL 32 b Induction Interactions also called screening This is the interaction of one subsys tem with the reaction field induced by another subsystem The interaction of the subsystem with its own reaction field is also part of the interaction and is used to calculate the polarization energy which is half the energy gain from ind
61. number of the property to be computed see Table 4 of Part 2 TAGA should be set to the TAG of one of the centres defined in in the ZMATRIX or GEOMETRY directive or in a CENTRES directive ISECT is the section number of the Dumpfile where the computed property integrals are to be stored If ISECT is omitted the integrals are not stored on the Dumpfile The final data line consists of the character string END in the first data field Only 100 property lines may be presented in any one job 3 2 CENTRES This directive permits the specification of additional non nuclear centres at which the prop erties are to be evaluated The first data line consists of the character string CENTRES in the first data field Subsequent data lines are read to variables X Y Z TAG using format 3F A where X Y and Z are the Cartesian co ordinates of an additional centre in atomic units TAG is a name up to 8 non blank characters by which the centre will subsequently be known TAG may be omitted when the system will supply an ordinal default The final line consists of the character string END in the first data field Example CENTRES 1 0 1 0 1 0 ADDC END 3 3 NUCLIDIC This directive is used to re define the nuclidic mass by the program which by default corresponds to the most abundant isotope The first data line consists of the character string NUCLIDIC in the first data field Subsequent lines are read to variables TAGB CENMAS using format A F TAGB sh
62. on classical surroundings c MORE More information on classical surroundings printing of DRF settings and flagging DRF additions to hamiltonian d MATRICES MORE plus DRF matrices produced e ONEEL MORE plus one electron information ra f TWOEL MORE plus two electron information The default is DRFOUT STANDARD NOTE This directive must proceed the EXTERNAL directive to be effective there 13 3 UNITS The UNITS directive specifies the unit of length used throughout the REACT input directives The directive consists of a single data line read to the variables TEXT UNIT using format 2A 1 TEXT should be set to the character string UNITS 13 DRF DIRECTIVES 37 2 UNIT can be set to the character strings BOHR or ANGS The default is UNITS BOHR NOTE All REACT subdirectives will be assumed to be in the units given here e g DSTGRP 15 will assign 15 Bohr to DSTGRP if UNITS BOHR but 15 Angstrom if UNITS ANGS is specified NOTE This directive must proceed the EXTERNAL directive to be effective there 13 4 GAMDRF The GAMDRF directive serves to specify the scaling factor to be applied to the estimate of the dispersion energy see also section 12 4 A non zero value also triggers the use of the Direct rather than Average Reaction Field coupling scheme The directive is read to the variables TEXT VALUE using format A F 1 TEXT should be set to the character string GAMDRF 2 VALUE is the scaling factor to be appli
63. or each specification of RUNTYPE ANALYSE Note that the original restrictions in running this module to basis sets comprising only s p and d basis functions have been lifted in the calculation of both molecular densities and potentials where the full range of s p d f and g functions may now be used The subsequent directives are presented in groups with the following functions 1 Those that define the grid of points a group of directives initiated by GDEF 2 Those that request data calculation on a grid a group of directives initiated by CALC 3 The SURF directive for generation of molecular surfaces a combination of both grid definition and calculation 4 The RESTORE directive to retrieve grid definitions or data from the dumpfile 5 Those that generate graphical output when available initiated by PLOT Presentation of each of the directives which appear as groups are initiated by the specific directives GDEF CALC and PLOT as given above Directives within a group are terminated by the first directive of another group by SURF or RESTORE or by any other valid GAMESS UK Class 2 directive The ordering of groups is significant but the ordering of directives within a group is not as follows 1 ACALC directive must be preceded by a directives to generate or restore a grid definition which will be used for the calculation An exception is a calculation of a combination grid TYPE COMB which must follow the definition
64. orm conical shape function 4 AFCT to specify the width parameter the value following the keyword With EXPO the width parameter is the exponential prefactor with CONE the width parameter is the radius of the cone Beyond this radius the charge distribution behaves as a point charge The type of damping function used CONE or EXPO also determines the default atom polariz abilities assigned to classical atoms see also 12 1 and possibly radii assigned to both QM and classical atoms see subdirectives QMRADI and CLASRADI If DAMPING OFF the polarizabilities belonging to the damping function associated with the conical charge distribution will be used The default is DAMPING OFF AFCT 1 662 NOTE This directive must proceed the EXTERNAL directive to be effective 13 15 CLASDISP The CLASDISP directive serves to specify the treatment of the dispersion interaction between the classical atoms and groups The directive consists of a single data line read to the variables TEXT n INTOPT using format nA 1 TEXT should be set to the character string CLASDISP 2 INTOPT may be either blank or one of following keywords a GROUPPOL or ATOMPOL to switch between the use of group polarizabilities and atom polarizabilities If there are polarizable atoms that are not used in the construction of any group polarizability the dispersion between those atom polarizabilities and any group polarizabilities is calculated if the GROUPPOL option is specif
65. ot change the configuration of the atom used in the atomic SCF calculation but will result in modification of the occupa tions of the atomic orbitals just prior to the computation of the density The computed density therefore does not correspond to a self consistent atomic calculation Example The atomic configuration chosen by default for the carbon atom would be 1s 2s 2p 0 866667 2p 0 666667 2p 0 666667 and for the iron atom dfs high spin 1s 2s 2px 2py 2pz 3s 3px 3py 3pz 4s 6 GRAPHICAL ANALYSIS 19 3d Sd 3d 2 3d2y2 3d 2 The CONFIG directive consists of three types of data line The first line the directive initiator consists of the character string CONFIG in the first data field the last line the directive terminator consists of the character string END in the first data field Lines specified between the directive initiator and terminator are the configuration definition lines If there are NAT atoms whose configuration are to be specified NAT configuration lines are required Each line consists of NORB 1 data fields where NORB is the total number of doubly occupied or partially occupied orbitals in the atom The first data field is read to the variable ALAB using format A whilst the remainder of the data line should contain real numbers read in F format to a vector OCC I l 1 NORB ALAB should be set to the label parameter of the nucleu
66. ould be set to the TAG of a previously defined atomic centre while CENMAS should be set to the value of the nuclidic mass to be used for this centre The final line consists of the character string END in the first data field Example 4 SIMPLIFIED PROPERTY SPECIFICATION 3 NUCLIDE OXYGEN 17 END 4 Simplified Property Specification In the section above we have assumed that property evaluation is to be conducted under control of RUNTYPE ANALYSE with explicit specification of the required one electron properties A simplified mechanism for property evaluation can be requested through presenting the data line PROPERTY ATOMS after RUNTYPE and SCFTYPE specification This will result in the default wavefunction anal ysis conducted after RUNTYPE processing being augmented with the computation of certain one electron properties The following points should be noted e the properties evaluated include the electrostatic potential electric field electric field gradient and electron density at each of the atomic centres plus the dipole second moment quadrupole moment third and octupole moments at the computed centre of mass of the system under study In addition the spin densities will also be computed in the case of open shell systems e this analysis if requested is available on completion of SCF OPTIMIZE OPTXYZ SADDLE and Cl processing e in contrast to the detailed property evaluation performed under RUNTYPE ANALYSE control t
67. pecify those molecular orbitals whose analysis is to be printed If NMO is the total number of orbitals whose analysis is required subsequent data fields should contain NMO integer numbers read in free l format An abbreviated form form of this data specification allows the user to introduce the character string TO read in free A format when specifying a sequence of consecutive orbitals The last data field presented should be the character string END Note that the integer and END data fields may be omitted in which case only the Mulliken analysis of the total wavefunction will be printed The following notes may be helpful e Each molecular orbital is individually analysed as if it contained one electron The oc cupation numbers as retrieved from the Dumpfile section nominated on the VECTORS directive are only used in the evaluation of the Mulliken populations of the total wave function e While all molecular orbitals regardless of occupation number are analysed the detailed analysis of a given orbital will only be printed if that orbital is referenced by the MULLIK directive Example 1 MULLIK ATOM ORBITAL 2 3 4 5 6 7 9 END Requests an atom and orbital group based analysis for molecular orbitals 2 to 7 inclusive plus molecular orbital 9 Example 2 The data line below has an equivalent effect to that of Example 1 MULLIK ATOM ORBITAL 2 TO 7 9 END 9 DISTRIBUTED MULTIPOLE ANALYSIS 28 has an equivalent effect to that of E
68. reated system The block is closed with an END directive The attributes of each atom in the classically treated system are input on a single data line in the following order but with free format first 2 character strings then 6 numerics name 2 parts charge x y z co ordinate polarizability radius 1 name The name of a classical atom consists of two parts a chemical symbol The chemical symbol is a maximum of 2 characters Apart from the elements classical points may also be named XX QQ and E which give them special attributes i QQ point charge only no polarizability no radius polarizability and radius given on the data line are ignored nominal unit polarizability for use in damping function only ii XX point charge with default unit polarizability and unit radius polarizability and radius given on the data line are effective iii E point charge and polarizability no radius radius given on the data line is ignored NOTE The extra atoms without radius QQ and E are ignored in the calculation of the model repulsion XX atoms do partake in the repulsion they are assigned 1 va lence electron For use in the Slater Kirkwood formula for the dispersion interaction E atoms are assigned 1 valence electron b group name The group name serves three purposes i to exclude interactions between classical atoms The exclusions are controlled by the first part of the group name the first
69. rj is the distance between atoms 7 and 7 The parameters used here do not come from the CHARMM force field but are instead the DRF parameters Several options for setting the radii and polarizabilities are available A special treatment of H bonds is possible as in the CHARMM force field The radius of the H atom participating in a H bond may be set differently from other H atom radii 12 4 Estimate of the Dispersion Interaction The interaction of the QM system with the polarizable environment is calculated by taking expectation values of the reaction field operator over the wave function The expectation values are of two kinds 9 10 12 FEATURES OF THE DRF MODEL 34 1 average the interaction of the charge density as a whole with the dipole moments induced by the charge distribution as a whole at the polarizability in formula OF 0 a 0 F 0 where 0 is the wave function F the electric field operator and a the polarizability 2 direct the screening of the self interaction through the interaction with the polarizable surrounding in formula OLF y af 0 The availability of these two expectation values enables an estimate of the dispersion interaction between QM systems and surroundings through a fluctuation expression Eaisp prr 3 O F t aF 0 OF t 0 0 0 F 0 The factor gt comes in when accounting for the polarization costs This expression may be rewritten in the same form as the second order p
70. rnal Points Points that carry point charges and polarizabilities may be grouped together Interactions between members of the same group e g a molecule may be excluded Also the dimensionality of the coupling matrix may be reduced by using group polarizabilities rather than atomic polarizabilities For instance for a classical surroundings comprising of any number water molecules described by 3 atoms each a reduction of a factor 3 in the dimensionality of the coupling matrix may be achieved by using one molecular polarizability for each water molecule For small molecules the results from using group polarizabilities do not differ considerably from using distributed atomic polarizabilities if the molecules are distant enough from the inducing electrostatic field Criteria for grouping may be supplied by the user and groupings may be suggested which are then tested against the criteria Grouping may also be enforced Thole has shown that for small organic molecules group polarizabilities from atom polarizabilities yield very good molecular polarizabilities compared to experiment 8 He derived a number of 12 FEATURES OF THE DRF MODEL 33 parameter sets for the atomic polarizabilities based on an assumption about the charge density distribution around an atom The shape of the charge density modifies the field at atoms within the molecule due to dipoles induced at other atoms in the molecule The density shape functions implemented her
71. s as specified by the corresponding nucleus definition lines in the GEOMETRY or ZMATRIX directives OCC I should be set to the occupation number of the i th atomic orbital The latter must be input in order of symmetry s p d etc with the partially occupied orbitals preceded by the doubly occupied orbitals within each symmetry class Example 1 Suppose the user wishes the 1s 2s 2px 2p configuration for a carbon atom which has been labelled as nucleus C1 Then the following configuration definition line should be specified Ci 2 0 2 0 1 0 1 0 0 0 Example 2 To specify the configuration 1s 2s 2p 3s 3p for an aluminium atom labelled AL by the ZMATRIX directive the user must specify the following configuration definition line AL 2 0 2 0 2 0 2 0 2 0 2 0 0 0 0 0 1 0 where the first three 2 0 give the occupation of the s orbitals and the remainder details the occupation of the p orbitals Example 3 To specify the configuration 15 25 2p 3s 3p 4s 3day 3dzz 3dyz for an iron atom which has been labelled FE the user should specify the following line FE 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 0 0 0 0 lt s orbitals gt lt p orbitals gt lt d orbitals gt Note that the occupation numbers of the three p orbitals should be input in the order x y z and those of the five d orbitals in the order dzy daz dyz dr2 y2 dz2 6 GRAPHICAL ANAL
72. s aken ede a abor ht 652 TYPE SPHERE ns ann ara Be OR ae A EA Ae 65 3 TYPE CARDS heards gt soa varaan etn ae een e a a 654 TYPE CONTOUR Valle s sa por orn aranea IE mat en ds 65 5 TYPE WRAP valie ee oen ida 229 444 4485 6 48 8 Grid Definition ORIG 2 0 2 e Grid Definition X and Y en Grid Definition SIZE e s o naob Daa a e gia Grid Definition POINTS lt ioi mur a ee Oa Ss Grid Definition SECTION 2 2 2 2 Directives Requesting Data Calculation o o a Data Calculation CALC a aa ocs pea ea daa a a i a e e a Data Calculation TITLE aaa 2 e Data Calculation TYPE ecs ade ea etn aren He a amp 6 14 1 MO and GRAD M ess oaeen ka a BALS COME 2 cote ss ee WE teh Ae e ESS 6 14 3 Van der Waals functions o e Data Calculation OCCDEF 000000 2b Data Calculation CONFIG 2 o e Data Calculation SFAG os eas haat aten a sa al Data Calculation RADI e ae a uy aen Bt el ater ea at ee Ht Data Calculation SECTION 2 464 be eee he ee ae CONTENTS 6 20 Data Calculation RESTORE lt gt s a omm tene ea bad a a ee e 6 21 Data Calculation SURF lt pioa cesma an a det a ele ala 6 21 1 Example Potential on an isodensity grid 6 22 Plot Requests lt 2 ene ne a A A AR ee A A 6 23 Plot Requests PLOT a 6 24 Plot Requests TITLE i A aen oen rs ol ie ele Se ae ok aN 6 25 Plot Requests TYPE oe an em deden hd
73. s between the QM and classical systems are cut and the QM system is capped by H atoms to satisfy valence These aspects of embedding are the subject of ongoing research Having decided on the QM system and the representation of the surroundings the embedding may be treated at the following levels 1 electrostatic potential as a perturbation The QM density is calculated as if the QM system were in vacuum The interaction with the point charges is then calculated with the vacuum density 2 electrostatic potential and reaction field as a perturbation The QM density is calculated as if the QM system were in vacuum The interaction with the point charges polarizabilities and dielectric is then calculated with the vacuum density 3 electrostatic potential self consistently The QM density is calculated in the presence of the potential generated by the point charges by including this field in the one electron hamiltonian 4 electrostatic potential self consistently and reaction field as a perturbation The QM density is calculated in the presence of the potential generated by the point charges by including this field in the one electron hamiltonian The interaction with the polarizabilities and dielectric is then calculated with this density 11 TOTAL ENERGY IN THE DRF MODEL 31 5 electrostatic potential and reaction field self consistently The QM density is calculated in the presence of the potential generated by the point charges and t
74. s defined for the reaction field induction interaction in this expression and the CHARMM repulsion as well 12 5 Expansion of Fields In this DRF implementation the electrostatic and reaction field operators of the QM charge dis tribution are expanded to second order which greatly reduces the computational effort because 13 DRF DIRECTIVES 35 the coupling equations need to be solved only for a limited number of source multipoles at each expansion centre rather than for every single overlap distribution Each overlap distribution is assigned to an expansion centre for which the static and reaction fields are calculated in advance for a unit charge dipole and quadrupole These formal interactions are then simply multiplied by the overlap dipole and second moment integrals of the charge distribution s in question to yield one and two electron matrix elements 1 By default the nuclei of the QM system are used as expansion centres but the user may add expansion centres by hand or by automated procedures Exact interaction with point charges may be obtained through using the BQ centres see 3 8 4 specified in the ZMATRIX directive As far as the DRF model is concerned these BQ centres are part of the QM system 12 6 Dielectric Response The dielectric response due to the continuum surrounding the molecular system may be calcu lated separately for the static and optic components in a single calculation To this end the two
75. surfaces The gradient functions generate unit normals to the surface ie not strict gradients but normals to the surface which are adequate for lighting calculations The internal van der Waals radii are taken from Nuffield Advanced Science Book of Data R D Harrison ed 1988 Additional or replacement radii may be provided using the RADII directive see below The two functions available are VDW defined by max WU r 6 GRAPHICAL ANALYSIS 17 and LVDW defined by max In r red where r is the distance from the test point to nucleus i red the van der Waals radius of atom i and the max function runs over all nuclei in the molecule Both functions have the property that the isovalue surface for value 0 0 is the van der Waals surface When contoured at a positive value v the VDW function gives rise to a surface inside the van der Waals surface corresponding to a surface with all radii reduced by v Similarly negative contour heights may be used to generate surfaces with a constant added to all radii Although not identical these surfaces are similar to Connolly surfaces with a probe sphere of radius v Contouring the LVDW function at non zero values gives rise to surfaces that correspond to scaled van der Waals radii Positive values v thus lead to surfaces inside the van de Waals radius NB It is important to note that at the moment the use of the LVDW function to generate the surfaces with scaled radii is not f
76. t regions of space surrounding it provides information about possible sites involved in protonation or in reactions with electrophilic agents The interaction energy between a molecular distribution and an external unitary positive charge at a given point i is given by nucl V ri 5 f Jan e 7 where Za is the nuclear charge of nucleus alpha and p 1 is the first order density function The program permits the construction of plots of electrostatic interaction energies based on the density distribution arising from wavefunctions constructed in Gaussian orbital basis sets 6 14 1 MO and GRAD MO The MO and GRAD MO keywords must be followed by an integer specifying the MO of interest 6 14 2 COMB The COMB keyword is followed by specification of the data to be combined with the current grid and a scale factor as follows TYPE COMB lfn iblk isec scale If lfn and iblk are given they determine the foreign dumpfile and start block on which the data is to be found If they are omitted the current dumpfile is used sec is the section number of the required data as specified using the SECTION directive when the data was generated The grid is multiplied by scale before being added to the current grid If more than two grids are to be combined Only one TYPE COMB directive may be present in a given CALC group of directives 6 14 3 Van der Waals functions These functions are defined in such a way that contouring them leads to VdW
77. uction at equilibrium c dispersion interactions an estimate of the dispersion energy between QM and clas sical subsystems based upon the Second order Perturbation SOP expression for the dispersion interaction may be calculated see also section 12 4 d model repulsion energy a molecular mechanics force field expression from CHARMM 7 is used to model Pauli repulsion between subsystems NOTE Electrons do not feel the repulsion and care has to be taken to avoid close contacts which may lead to electrons wandering off the QM system Devices to lessen this effect are available see section 12 2 Care should be taken in comparing total energies that the proper reference systems have been defined In a single calculation one does not have access to the polarization energy of the QM system this is the change of the expectation value of the vacuum hamiltonian of the QM distribution and therefore internal QM energy upon interaction with the surroundings A separate calcu lation in the absence of the surroundings or with the effect of the surroundings treated as a perturbation only is necessary to obtain this interaction energy The definition of the zero of energy for the classical system has been discussed above The total energy of QM classical system is given on output under configuration total energy Contributions have been described in the Output section 14 12 Features of the DRF Model 12 1 Grouping of Exte
78. ully tested ie there are sets of radii and or choices of contour levels which will result in a surface that does not correspond to that generated from the scaled radii 6 15 Data Calculation OCCDEF The purpose of this directive is to allow the user to define the occupation numbers for the molecular orbitals to be analysed In the absence of the OCCDEF directive the occupation numbers will be taken from the section of the Dumpfile specified on the VECTORS directive The first data line contains the character string OCCDEF in the first data field Following the directive initiator are the occupation definition lines The first data field of such lines is read in F format and should contain a specified occupation number Subsequent data fields are read in I format Let the value of an integer specified in such a field be j the j th molecular orbital will be assigned the occupation number specified in the first data field of the line The following 2 0 1234657 comprises a valid occupation definition line Such lines may be shortened if a sequence of consecutive integers appear by means of the character string TO Thus the abbreviated form of the above line is 2 0 1 TO 5 7 The occupation definition lines are specified until all the orbitals to be assigned a finite occupancy have been declared A data line containing the text END in the first data field must be specified to terminate the OCCDEF directive The following points
79. urther removed the whole group is discarded 13 DRF DIRECTIVES 40 The default is DSTMAX 1000 0 NOTE This directive must proceed the EXTERNAL directive to be effective 13 11 AGRPE The AGRPE directive specifies the polarization energy difference criterion for constructing group polarizabilities from atomic polarizabilities under the control of the GROUPING directive The directive consists of a single data line read to the variables TEXT AGRPE using format A F 1 TEXT should be set to the character string AGRPE 2 AGRPE is the maximum allowed energy difference between the reaction field interaction of a unit charge at the nearest QM atom as calculated with and without the grouping If the energy difference is larger grouping is not effected The default is AGRPE 0 001 in Hartree NOTE This directive must proceed the EXTERNAL directive to be effective 13 12 AGRPM The AGRPM directive specifies the induced dipole difference criterion for constructing group polarizabilities from atomic polarizabilities under the control of the GROUPING directive The directive consists of a single data line read to the variables TEXT AGRPM using format A F 1 TEXT should be set to the character string AGRPM 2 AGRPM is the maximum allowed induced dipole difference between the induced dipole due to a unit charge at the nearest QM atom as calculated with and without the grouping If the induced dipole difference is larger grouping is not eff
80. uum If the solvent is known solvent properties will be taken from the internal database Values in the internal database supersede any other input The directive is read to the variables TEXT SOLNAM using format 2A 1 TEXT should be set to the character string SOLVENT 2 SOLNAM is the name of the solvent associated with the dielectric continuum more than 8 characters are permissible An internal database storing solvent static and optic dielectric constants molecular masses and densities is accessed through this directive Specification of an unknown solvent will result in discontinuation of the calculation except when SOLNAM X is specified The default is SOLVENT X 13 19 7 DIELTYP The DIELTYP directive serves to specify the types of dielectric response taken into account Static and or optic dielectric response may be taken into account If the estimate of the disper sion energy is requested see GAMDRF directive the appropriate direct reaction field coupling of the electrons is only to the optic part of the dielectric response if the optic response is requested The directive is read to the variables TEXT DIELOPT1 DIELOPT2 using format 3A 1 TEXT should be set to the character string DIELTYP 2 DIELOPT1 and DIELOPT2 are the types of response requested Either may be set to STAT or OPT or left empty requesting static and or optic response and absence of response respectively The default is DIELTYP STAT 13 DRF DI
81. vector section usage removing the need for explicit section specification on both the VECTORS and ENTER directives in such jobs the user is strongly advised to specify the section containing the eigenvectors to be analysed under RUNTYPE ANALYSE With the exception of Localised Orbital generation the analysis routines do not output a separate set of eigenvectors so that no section specification is required on the ENTER directive In such cases the following sequence is typical of that required VECTORS 1 ENTER with the eigenvectors to be analysed resident in section 1 In the case of localised orbital generation the sequence VECTORS 1 ENTER 10 will act to route the localised orbitals to section 10 of the Dumpfile Each mode of analysis has an associated set of sub directives which are described below 3 ONE ELECTRON PROPERTIES 2 3 One electron Properties This section deals with the data input used to drive the 1 electron properties module Note that the module can at present only run with basis sets comprising s p and d basis functions see however the simplified property specification described below 3 1 PROPERTY This directive is used to specify which molecular 1 electron properties are to be computed The first data line consists of the character string PROPERTY in the first data field Subsequent data lines the property definition lines are read to variables NPROP TAGA ISECT using format 1 A 1 NPROP is a code
82. xample 1 Example 3 The following data line will request an atom grouped analysis for the total wavefunction alone with no printed analysis of the individual orbitals MULLIK ATOM 9 Distributed Multipole Analysis The DMA analysis 5 is instigated by the directive DMA By default the DMA module will generate an expansion with multipoles at the atomic sites with a maximum value rank of 10 for the poles at each site Each site is assigned a relative radius see below which is used in the partitioning of the overlap density between the sites By default all relative radii are set to 1 0 A number of subdirectives may be presented after the DMA line these serve to modify the selection of DMA sites and the distribution algorithms for partitioning between the sites 91 ADD ADD name x y z lt lmax lt radius gt gt Add a new site at x y z with the name specified the multipole rank is limited to Imax if a value is specified and a relative radius can be specified also 9 2 DELETE DELETE name Delete all sites of the given name DELETE ALL deletes all sites DELETE CHARGE deletes nuclear charges on the atoms 93 RADIUS RADIUS name radius Specify a relative radius for all sites with the name given The actual distances from an overlap centre to the sites are scaled by dividing by the relative radii of the sites and the contributions are moved to the site which is closest in terms of scaled distances to the overlap

GAMESS-UK USER'S GUIDE and REFERENCE MANUAL Version

Contents

Download Pdf Manuals

Related Search

Related Contents