TeraChem User's Guide
Contents
1. Because the binary file is linked against the Intel MKL library it is recommended to run TeraChem on Intel based workstations The amount of CPU RAM needed depends on the size of the molecules that will be studied If the molecules of interest are relatively small less than 500 atoms the usual 8Gb or 16Gb configuration is acceptable For very large molecules in excess of 10 000 basis functions CPU RAM will often be a limiting factor For example molecules with 25 000 basis functions require almost 70GB of CPU memory Installation First obtain and install the latest CUDA driver TeraChem 1 5K requires 304 54 or later and the CUDA 5 0 toolkit choose the one appropriate for your Linux OS e g RedHat Enterprise Linux 5 5 for RHEL 5 5 or CentOS 5 5 available for download free of charge at https developer nvidia com cuda downloads If CUDA 5 0 is not installed on your machine and you do not have root permissions you can install the toolkit in your home directory and set LD_ LIBRARY PATH environment variable accordingly export LD LIBRARY PATH cuda 1ib64 LD LIBRARY PATH Installation of the CUDA driver must be performed by a user with root permission i e the superuser Check with your local system administrator first since adequate CUDA drivers may already be installed Make sure you select the 64 bit Linux operating system You will need to install the CUDA driver and the CUDA toolkit ver 5 0 The CUDA SDK is not required2. but also includes the basis functions for fragment B but not the electrons or nuclei corresponding to the atoms of B In TeraChem one can include ghost atoms atoms which contribute basis functions to the calculation but not electrons or nuclear charges by prefacing the element name with the letter X For example the following is a coordinates XYZ file used in calculating the counterpoise corrected interaction energy for water dimer 6 O 0 029481 0 086991 0 533710 H 0 660044 0 772698 0 712077 H 0 086741 0 049151 0 406478 XO 0 306708 0 307377 2 262155 XH 1 109626 0 019913 2 679671 XH 0 049150 1 088298 2 668550 The last three atoms will be ghost or dummy atoms i e the system has only 10 electrons one oxygen atom nucleus and two hydrogen atom nuclei but basis functions will be used on all six listed atoms according to the basis set listed in the start file Geometry Optimization and Transition State Search The instdir tests sp directory contains a simple configuration file start go used for geometry optimization of a spiropyran molecule basis set basis 6 31g coordinates file coordinates sp xyz molecule charge charge 0 SCF method rhf blyp b3lyp etc RHF method rhf type of the job energy gradient md minimize ts geometry optimization run minimize end The optimization is triggered by the minimize keyword Note that the sp xyz file in fact contains two sets of coordinates f
3. B 66 155115 2002 S Grimme J Comp Chem 27 1787 2006 12 S Grimme J Antony S Ehrlich and H Krieg J Chem Phys 132 154104 2010 TeraChem User s Guide Page 26 2009 2012 PetaChem LLC TeraChem User s Guide memory e g GeForce Use at your own risk Geometry Optimization and Transition State Search min print How much output is desired verbose something verbose debug nstep Maximum number of optimization TS search steps 100 min_tolerance Termination criterion based on the maximum energy RO gradient component min_tolerance_e Termination criterion based on the SCF energy Lg change min_coordinates Type of coordinates in which optimization TS search is performed dlc cartesian dlc dlc_tc hdlc hdlc_tc min_method Optimization TS search method sd cg1 cg2 1bfgs sd steepest descent lbfgs cg1 and cg2 conjugate gradient lb gs L BFGS min_hess_update Hessian update algorithm never powell bofill bfgs bfgs If never the Hessian is recalculated using finite differences at each step min_init_hess Initial Hessian fischer almlof one point two point diagonal identity one two point exact Hessian from finite differences diagonal only diagonal elements are calculated fischer using final differences off diagonal elements equal almlof zero identity initial Hessian is an identity
4. Constrained coordinates will be constrained to the value they have in the starting geometry basis set basis 6 319 coordinates file coordinates C10H22 inp molecular charge charge 0 optimize geometry run minimize end Sconstraints bond connecting atoms 32 and 29 bond 32 29 32 29 26 angle angle 32 29 26 32 29 26 27 dihedral dihedral 32 29 26 27 Send Finally it is straightforward to freeze all hydrogen or non hydrogen atoms by atom hydrogens or atom heavy respectively TeraChem User s Guide Page 18 2009 2012 PetaChem LLC V Trajectory visualization To create a simple MD trajectory you can use the example in instdir tests caffeine The configuration file start md is basis set basis 6 31lg coordinates file coordinates caffeine xyz molecule charge charge 0 SCF method rhf blyp b3lyp etc DFT BLYP method blyp type of the job energy gradient md minimize ts MD run md number of MD steps nstep 10 dump orbitals every MD step orbitalswrtfrq 1 end The only difference between this file and the file used for the single point calculations are the nstep and orbitalswrtfrq parameters which are now set to 10 and 1 respectively The keyword orbitalswrtfrq ensures that the molecular orbitals will be written at every MD step out of 10 total The TeraChem output coordinates file format is compatible with VMD To open the trajectory file go to VMD gt File gt New Molecule Brows
5. is the climbing image 10 Molecular dynamics parameters nstep Total number of MD steps Set nstep to 0 for single point energy calculations integer 10 integrator The way the initial WF guess is generated in subsequent MD iterations In the first several iterations the initial guess is constructed from scratch reversible d reversible regular reset reversible d time reversible integrator with dissipation S w reversible time reversible integrator without dissipation regular initial WF guess is taken from converged reversible d B A MLN Niklasson et al J Chem Phys 130 214109 2009 14 A M N Niklasson et al Phys Rev Lett 97 123001 2006 TeraChem User s Guide Page 28 2009 2012 PetaChem LLC TeraChem User s Guide WF at previous MD step reset initial WF guess is generated from scratch at each MD step rseed Seed for random number generator Set this to a different integer for different MD runs or set it to a known seed in order to reproduce an earlier run 1351351 timestep MD integration time step in femtoseconds float thermostat Temperature control velocity rescaling or Langevin dynamics rescale or langevin rescale rescalefreg When velocity rescaling is used determines how often the velocities are rescaled For instance setting rescale to 1000 will force rescaling at every 1000 MD step
6. projected onto projectbasis and stored in scr prict file scr prjcta scr prjctb in unrestricted methods not set charge The total charge of the molecule integer not set spinmult Spin multiplicity 2s 1 of wavefunction integer method Restricted unrestricted and restricted open shell HF and KS Restricted wavefunction rhf svwn blyp b3lyp b3lyp1 b3lyp5 pbe revpbe pbe0 revpbe0 wpbe wpbeh bop mubop camb3lyp b97 wb97 wb97x b3lyp or b3lyp1 VWNI correlation b3lyp5 VWNS correlation Unrestricted calculations are invoked by adding u prefix i e uhf ublyp ub31lyp ete Restricted open shell calculations are invoked by adding ro prefix i e rohf roblyp rob31yp etc rhf TeraChem User s Guide Page 24 O 2009 2012 PetaChem LLC TeraChem User s Guide rc w Range correction scaling parameter required by DFT functionals with a fraction of exact long range exchange operator depends on DFT functional Long range exact exchange operator contribution depends on DFT functional dftgrid Integer value within 0 5 range inclusive Larger numbers are denser grids and hence provide more accurate results Grid 0 contains 800 grid points atom and grid 5 contains 80 000 points per atom The default grid type 1 contains about 3 000 points per atom dynamicgrid yes no This parameter enables use of dynamical DFT grids When
7. then project the solution onto the desired basis set and start another SCF procedure using the projected wavefunction as initial guess Below is an example of such project job Here the calculations are performed in a smaller sto 3g basis set and the converged wavefunction is projected onto 6 31g basis set run project basis sto 3g projectbasis 6 31g charge 0 coordinates water xyz end The projected wavefunction is stored in scr prjct file MD with spherical boundary conditions In an MD simulation it is possible to impose spherical boundary conditions to prevent evaporation events or constrain a system to a given density The spherical boundary conditions are provided in the form of a sum of two harmonic terms U onsi r k r E Reener R y k r R ie R y gt where Reenter 1s the center of mass of the system calculated for the first MD frame and then fixed By default k is set to 10 0 kcal mol A and k is set to zero The simplest way to impose spherical boundary conditions is to set mdbc spherical md_density 1 0 in the start file ma density specifies the density of the system in g mL used to automatically adjust Ri Ifmd_ density is not provided R needs to be set explicitly using the md_r1 keyword Note that constraining forces are not applied to hydrogen atoms QM MM Functionality Limited QM MM functionality is available in this release Only water molecules are available for MM treatmen
8. 9 0 0022302215 0 0001021822 01 9996468643 91 9674933789 680 2039760440 0 76 10 0 0005471869 0 0000498203 01 9996473056 91 9698688887 680 2040258644 0 56 THRESPDP set to 3 56e 03 TT 0 0002710918 0 0000079054 01 9996488341 91 9703058755 680 2040179590 0 74 12 0 0001137490 0 0000014169 01 9996487467 91 9698501918 680 2040193759 0 65 13 0 0000577038 0 0000001696 01 9996487669 91 9696944751 680 2040195455 0 68 14 0 0000185995 0 0000000001 01 9996487389 91 9698173292 680 2040195456 0 64 DISPERSION CONTRIBUTION TO ENERGY 0 0562114195 a u FINAL ENERGY 680 2040195456 a u CENTER OF MASS 0 008017 0 006143 0 000066 ANGS DIPOLE MOMENT 3 430559 0 664809 0 000035 D 3 494382 DEBYE Writing out molden info Running Mulliken population analysis Total processing time 7 94 sec Job finished Fri Dec 7 15 00 15 2012 lll TeraChem I O file formats Input files In addition to the start file containing job parameters TeraChem requires two other files to start a job coordinates and basis set Atomic coordinates The coordinates file fed to the coordinates parameter should be either in XMol or PDB format In an XMol coordinates file the first line specifies the number of atoms and the second line provides a description of the system it can be left blank Atomic coordinates are listed starting from the third line All coordinates are either in Angstroms default or Bohrs this can be specified in the start f
9. To obtain NVE dynamics set rescalefreq to a value larger than nstep 2 10 tinit Initial temperature K sampled from Boltzmann distribution of velocities at T tinit float 300 0 t0 Thermostat temperature K float 300 0 invtime The Langevin damping time fs only used when thermostat is set to langevin 1000 0 orbitals Path to an output file containing the canonical molecular orbitals The orbitals are printed in GAMESS format and can be visualized by VMD orbitals log molden Path to an output file containing the canonical molecular orbitals in Molden format molden molf orbitalswrtfrq Determines how often the orbitals are written to the output file Due to large size sometimes the orbitals require 100MB and even more of disk space it does not make sense to write orbitals at every MD iteration integer 2 10 velocities Filename containing initial velocities or random to specify that initial velocities should be drawn from Boltzmann distribution random restartmd Path to the MD restart binary file If set the data in this file rather than coordinates velocities temperature etc is used to start MD trajectory not set restartmdfreq Specifies how often the restart data is dumped to scr restart md 100 mdbc spherical Enables spherical boundary conditions not set TeraChem User s Guide Page 29 2009 2012 Pet
10. and 54321 the port specified by the imd keyword in the TeraChem input file in the Port field Click the Connect radio button and you should see TeraChem executing in its window while the benzene molecule vibrates in the VMD display window VII TeraChem job parameters Available job parameters are listed in Table 1 Note the use of the character which should be interpreted as or For example x y means that one of x or y should be entered Table 1 Available TeraChem job parameters Parameter Description Default value General parameters scrdir Scratch directory scr Zan Sets calculation type energy Single point energy project Wavefunction projection for better initial guess gradient Energy and gradient minimize Optimize geometry ts Transition state search ma Born Oppenheimer Molecular Dynamics energy gpus Number of GPUs to use in parallel Sometimes one needs to change the default order of the devices For example when device zero is used solely for display purposes In such cases the following line specifies which GPUs should be used the enumeration starts from 0 all gpus 3 132 or gpus 3 to use the default device order o 1 2 precision single mixed dynamic double By default TeraChem uses a dynamic precision scheme where two electron integrals larger than some threshold value are computed with double precision and the rest are comput
11. but may be installed for other purposes if desired After downloading the driver package shut down the X server by typing sudo init 3 Then launch the driver binary and follow the instructions Unpack the tc tar archive using the following command in a temporary directory which you may later remove S tar xvf tc tar Run the install script by typing TeraChem User s Guide chmod u x install install This script will verify that your machine has a suitable graphics card verify that you accept the license terms and install the software in a location of your choosing the TeraChem installation directory or instdir in the following The script will ask you for the location of the CUDA libraries installed when the CUDA toolkit is installed see above It will also create a script that sets the appropriate environment variables The install script will also put a temporary license file in place so you can begin using TeraChem immediately However this temporary license file is time limited so you will want to obtain a permanent license file The install script ends with a form suitable for emailing to help petachem com Institution Ordered By MAC 003048DB1D7E IP 171 64 125 189 You can regenerate this at any time by typing machid in the TeraChem installation directory Fill in the Institution and Ordered By fields and email to help Apetachem com When we receive this from you we wil
12. 1 00e 04 DFT Functional requested blyp Method BLYP with dispersion correction Becke 1988 exchange functional Lee Yang Parr correlation functional Wavefunction RESTRICTED 1 0 1 0 DFTD3 V2 0 Rev 1 S Grimme University Muenster Fri Dec 17 17 08 12 CET 2010 Hawaii Version Please cite DFT D3 work done with this code as S Grimme J Antony S Ehrlich and H Krieg J Chem Phys 132 2010 154104 If used with BJ damping cite also S Grimme S Ehrlich and L Goerigk JCC submitted For DFT D2 the reference is S Grimme J Comput Chem 27 2006 1787 1799 DFT grid type 1 Using dynamic DFT grids Initial guess generated by maximum overlap TKK KKK KK KK KK KK KK KK KKK RARA KARA KARA KARA KARA RA SINGLE POINT ENERGY CALCULATIONS FI I RI I I I Rk Ie using 2 out of 4 CUDA devices Device 0 Tesla K20c 5119MB CC 3 5 IDLE Device 1 Tesla C2050 3071MB CC 2 0 IDLE Device 2 GeForce GTX 690 2047MB CC 3 0 CPU THREAD 0 Device 3 GeForce GTX 690 2047MB CC 3 0 CPU THREAD 1 CPU Memory Available 9008 38 MegaWords GPU Memory Available 255 91 MegaWords Maximum recommended basis set size 11200 basis functions limited by GPU memory Using d functions Configuring GPUs accordingly 0 CUBLAS initialized available GPU memory 1347MB 1 CUBLAS initialized available GPU memory 1346MB TeraChem User s Guide Page 8 2009 2012 PetaChem LLC TeraChem User s Guide Basis s
13. Agreement shall be construed as creating of the relationships of joint venturers partners employer and employee franchisor and franchisee master and servant or principal and agent TeraChem User s Guide Page 34 2009 2012 PetaChem LLC TeraChem User s Guide Release Notes v1 50K Fixed memory allocation problem which caused CUDA errors when running on multiple cards with shells that had few basis functions e g when running with a single set of d functions over four cards Implemented workaround for NVIDIA s texture bug which caused Tesla C2075 and GeForce 580 GTX to hang randomly Although we still do not recommend these cards all tests so far suggest they can run TeraChem without errors Document the ability to use ghost atoms atoms that have basis functions but no electrons or nucleus used in computing basis set superposition error Document the ability to use matrix purification instead of diagonalization Added A DIIS DIIS convergence scheme TeraChem User s Guide Page 35 2009 2012 PetaChem LLC
14. BILITY ARISING OUT OF OR IN ANY WAY RELATED TO THE SOFTWARE THE PROVISION OF OR FAILURE TO PROVIDE TECHNICAL SUPPORT OR OTHERWISE UNDER OR IN CONNECTION WITH THIS AGREEMENT EVEN IF PETACHEM HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGE YOU ACKNOWLEDGE THAT THIS ALLOCATION OF RISKS IS A PART OF THE BARGAIN OF THIS AGREEMENT Notwithstanding PetaChem s total liability under or in connection with this Agreement and your exclusive remedy for all of the foregoing however arising is limited to direct damages up to the cost of the Software to you The foregoing limitations exclusions and disclaimers will apply to the maximum extent permitted by applicable law even if any remedy fails its essential purpose Some states do not allow the exclusion or limitation of incidental or consequential damages so the above limitations may be inapplicable to you 8 Export You may not use or otherwise export or reexport the Software except as authorized by United States law and the laws of the jurisdiction in which the Software was obtained In particular but without limitation the Software may not be exported or reexported a into any U S embargoed countries or b to anyone on the U S Treasury Department s list of TeraChem User s Guide Page 33 2009 2012 PetaChem LLC TeraChem User s Guide Specially Designated Nationals or the U S Department of Commerce Denied Person s List or Entity List By using the Software you represen
15. S 2 3 73407177E 01 7 17324343E 01 S 2 5 4471780 0 156284978695 TeraChem User s Guide Page 11 2009 2012 PetaChem LLC TeraChem User s Guide 0 8245472 0 904690876670 0 1831916 1 000000000000 When mixing basis sets the atom names in the coordinates file should be consistent with those provided in the basis files Here is an example of the corresponding XYZ file 2 Hydrogen Molecule H1 0 0 0 0 0 0 H2 0 7 0 0 0 0 Note that a user can use a local copy of the basis directory if desired by setting the TeraChem environment variable appropriately In that case one should also ensure that a copy of the license dat file exists in TeraChem Fixing Atoms in Molecular Dynamics It is possible to fix a number of atoms in molecular dynamics by listing the atom numbers in a file called ixed_atoms located in the directory containing the input file The format is simply the number of fixed atoms followed by the atom number counting starts at zero of each fixed atom with one atom per line The force on fixed atoms is simply zeroed out with no modification to the forces on other atoms Only QM atoms can be fixed in QM MM simulations This does not have any effect on optimizations Ab Initio Steered Molecular Dynamics AISMD Specific atoms can be subject to constant pulling forces to generate force modified potential energy surfaces or molecular dynamics on these FMPESs In order to accomplish this one needs to spec
16. TeraChem User s Guide Version 1 5K PetaChem LLC 26040 Elena Road Los Altos Hills CA 94022 http www petachem com Contents E TGP OC UC AAA no o ossos trossos oa sses seino ssri 3 Obtaining Tera Cha as 4 Citne Lera NGI A A anus tue tates 4 ARONA Md a Sobol Jalen ol a aah alu ota a Seb id Zlcue Sok taeda ta tate 4 WE Getting O covaissondsiecssossentesecses 5 System reg ireMmentS a A 5 A A ENEE 5 R nning soplo os ro i a 6 HI TeraChem I O file Tormats een 9 put A 9 A sae a E E Soa tue ots E e eo nutase E tem 9 SIS Set Mle doma tl os Se a enltuas ted aS 10 OPUS 0 SATA Aas tar Me dace dee cl Sedo BRA Ale AAA 12 IV More details on some TeraChem capabilities oomoomss 15 Wavef netion projection A A 15 MD with spherical boundary Conditionssiesos5 anes sina a 15 QM MM Fite tion A A deco tania dada 15 Int gration With NBO iieii eaaa EAE A NENEA E REAA AES EE e RNEER ES 16 A ER E E EA A OE a ey EE eee 16 Geometry Optimization and Transition State Search oooonnccninccnoncnnoccnoncconccconoconononn coo nono nocnnos 17 V Trajectory VISUALIZACIONES 19 VI Interactive calculations iio 22 VIL Tera Chem job parameter a 23 Contact information ad 31 COPE t 31 End user license agreement siii soseasosesuesced ssvosessevuscssevconssunduncss cendceseveusechisceeaveneus 32 Introduction TeraChem is general purpose quantum chemistry software designed to run on Nvidia CUDA enabled GPU architectures under a 64 bit Lin
17. aChem LLC TeraChem User s Guide md_density If set Rj is automatically adjusted to the specified E 1 0 density in g mL md_r1 md_r2 R and R2 parameters for spherical boundary toe 6 conditions in A md k1 md_k2 k and k parameters for spherical boundary conditions A in kcal mol A imd Invokes interactive molecular dynamics by specifying Bevel the corresponding VMD port TeraChem User s Guide Page 30 2009 2012 PetaChem LLC Contact information We will be pleased to receive any feedback on your experience with TeraChem Should you have any suggestions concerns or bug reports please email them to help petachem com Also please feel free to participate in the TeraChem User Forum at http www petachem com forum TeraChem developers monitor this forum frequently and are happy to answer questions about the software Copyright TeraChem software is Copyright 2009 2012 PetaChem LLC End user license agreement IMPORTANT PLEASE READ THIS END USER LICENSE AGREEMENT AGREEMENT CAREFULLY BEFORE DOWNLOADING INSTALLING OR USING THE SOFTWARE BY DOWNLOADING INSTALLING UPDATING COPYING OR USING THE SOFTWARE YOU AGREE TO BE BOUND BY THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT DO NOT DOWNLOAD INSTALL UPDATE COPY OR USE THE SOFTWARE l Grant of License Subject to the conditions and limitations set forth herein PetaChem LLC Pe
18. ce Bond Theory J Phys Chem 1994 98 p13498 In the AO block core orbitals cor are listed first followed by valence orbitals vaL Each atomic orbital thus is represented by Brs coefficients Therefore the total number of AO coefficients is equal to BFS COR VAL Basis shells including the shells type number of primitive functions and corresponding contraction coefficients and exponents are listed at the end of the atom description S 3 1447 4004110 0 1543289673 263 6457916 0 5353281423 71 35284019 0 4446345422 P 3 111 9194891 0 1559162750 26 00768236 0 6076837186 8 458505490 0 3919573931 D 3 6 411803475 0 2197679508 1 955804428 0 6555473627 0 754610151 0 2865732590 It should be noted that the ordering of basis functions in the AO expansion used to construct the initial guess must be the same as in the GTO block above Within P type shells the basis functions are ordered as X Y Z and within D type shells as XY XZ YZ XX YY ZZ It is straightforward to mix different basis sets for the same molecule To do that one needs to create a separate basis file which will contain all required basis functions Here is an example calculation of a hydrogen molecule with STO 3G and 3 21G basis set used for the first and the second hydrogen atom respectively ATOM H1 COR 0 VAL 1 BFS 1 1 00000000E 00 S 3 3 4252509 0 154328967295 0 6239137 0 535328142282 0 1688554 0 444634542185 ATOM H2 COR 0 VAL 1 BF
19. ction with a valid license from PetaChem LLC Use of this program or results thereof indicates acceptance of all terms and conditions stated in the license and that a valid license agreement between the user and PetaChem LLC exists PetaChem LLC does not warrant the correctness of results or their suitability for any purpose Please email bugs suggestions and comments to help petachem com FF FF FF HF OH TKK KKK KK KK KKK RARA RARA RARA RARA RARA RARA RARA RARA RARA KARA KARA RA KKK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK kk Compiled by toddmtz Fri Dec 7 00 14 47 PST 2012 Supported architectures SM 1 3 2 0 3 0 3 5 Cuda compilation tools release 5 0 V0 2 1221 KKK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KKK KKK KK KK KKK KKK KK KK KK KK AK Job started Fri Dec 7 15 00 03 2012 On MTZ08 available memory 68820 MB Aaa a A a aE a AE a a a a a a EEE E EEEE RUNTIME INFO AIE att AE AE AAE AE AE AEE AE a aH aa a a aE a AEE AE a a a a EHE terachem start NVRM version NVIDIA UNIX x86_64 Kernel Module 304 54 GCC version gcc version 4 3 2 20081105 Red Hat 4 3 2 7 GCC TeraChem User s Guide Page 7 2009 2012 PetaChem LLC Sat Sep 29 00 05 49 PDT 2012 TeraChem User s Guide linux vdso so 1 gt 0x00007fffcddaf000 libpthread so 0 gt 1ib64 libpthread so 0 0x000000382e400000 libcufft so 5 0 gt usr loca
20. ctory visualization is performed on a local desktop TeraChem can visualize the geometry optimization TS search and molecular dynamics trajectories in real time i e interactively as the calculations run These interactive molecular dynamics IMD runs are practical for molecules with up to approximately 20 atoms using a hardware solution with eight GPUs Future versions will also allow for user manipulation of the molecule i e imposing external forces on atoms In the instdir tests benzene directory you will find the files needed to try IMD for benzene The configuration file start imd reads basis set basis sto 3g coordinates file coordinates C6H6 pdb molecule charge charge 0 SCF method rhf blyp b3lyp etc Restricted Hartree Fock method rhf type of the job energy gradient md minimize ts MD run md initial temperature in K tinit 1000 this triggers interactive molecular dynamics imd specifies the port VMD should connect to imd 54321 number of MD steps nstep 1000 end Open two terminal windows In the first window launch VMD and load in the coordinates of the benzene molecule from C6H6 pdb In the second terminal window launch TeraChem which will initialize the simulation and pause for connection to be made with VMD Now in VMD select Extensions gt Simulation MIMD Connect NAMD Type localhost or the IP address of the remote machine on which TeraChem is currently running in the Hostname field
21. dinates caffeine xyz molecule charge charge 0 SCF method rhf blyp b3lyp etc DFT BLYP method blyp add dispersion correction DFT D dftd yes type of the job energy gradient md minimize ts run energy end energy All lines beginning with the character are considered comments and are ignored by TeraChem There is no requirement on the line ordering in the start file except that the last line should be end Below is the output from this example job The program first lists the parameters followed by all GPUs used in the job Each GPU has its amount of memory and compute capability printed next to it The program then attempts to predict the maximum size of the molecule that can be handled on the current machine based on the amount of available CPU and GPU memory Note that the recommended maximum size of the system is approximate The SCF procedure which includes the DIIS error the maximum component of the DIIS error vector integrated number of electrons exchange correlation energy SCF energy and the total time elapsed per iteration completes the program s output S terachem start KKK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KK KKK KKK KK KK KK KKK KKK KK KK KK AK 2 TeraChem v1 5K Hg Version b133f5bd52e3 ia k Compiled for GeForce Cards E h Chemistry at the Speed of Graphics le KARA KK AAA KK RARA RARA KKKK KK KK KKKK KK KKKKKK KK KKK KKK KK This program may only be used in conne
22. e to the output coors xyz file and make sure that the file type is correctly determined Otherwise select XYZ in the Determine file type menu After the trajectory is loaded you can adjust the representation settings so that the final molecule looks as shown in Figure 1 TeraChem User s Guide Ml Graphical Representatic Selected Molecule __ hd Create Rep Delete Rep Style Color Selection Selected Atorns fan Draw style Selections Trajectory Periodic Coloring Method Material Name Iv 0paque y Drawin Method CEE Default Sphere Scale Y ij 10 gt Sphere Resolution 4 y 23 gt Bond Radius y 0 3 Bond Resolution 4 y 21 gt Apply Changes Automatically Apply COS 10 x File Molecule Graphics Display Mouse Extensions Help ID T A D F Molecule Atoms Frames Vol 2 TAD orbitals log 24 1 0 ie step 4 1 H speed leh 4 41 zoom r Loop xy Figure 1 Caffeine molecule geometry output coors xyz in VMD The molecular orbitals can be visualized with VMD in similar fashion Again go to VMD gt File gt New Molecule Browse to the output orbitals log file and make sure that the determined file type is GAMESS Otherwise select GAMESS in the Determine file type menu To display both positive and negative isosurfaces you will need to create two representations for eac
23. ed with single precision The threshold which determines the splitting between dynamic single precision and double precision evaluation of the integrals is determined automatically during the SCF calculation The mixed precision scheme uses a static threshold to determine which integrals should be evaluated in double precision those larger than threspdp which can be set in inputfi1le Users can TeraChem User s Guide also request to use full single or double precision depending on the job purposes Note that accumulation of all quantities on GPU is always performed with double precision accuracy to avoid floating point summation errors threspdp Threshold used to split single and double precision work in mixed precision calculations atomic units 0 001 coordinates Name of file containing atomic coordinates not set qmmm Name of file containing MM water coordinates The presence of this keyword triggers a QM MM calculation not set basis All available basis sets are located in basis directory In addition users can construct customized basis sets Here are examples of correct entries sto 3g 6 31 G 6 311 G 3df 3pd aug cc pvdz mini s midi When the string is parsed all symbols are replaced by s and all parenthesis are replaced by brackets to comply with Unix file naming rules not set projectbasis In project jobs the converged wave function is
24. et 6 31gs Total atoms 24 Total charge 0 Total electrons 102 5l alpha 51 beta Number electrons modeled by ECPs 0 Total orbitals 230 Total AO shells 104 62 S shells 28 P shells 14 D shells 0 F shells 0 G shells Spin multiplicity 1 Nuclear repulsion energy QM atoms 933 356431723822 a u Setting up the DFT grid time to set the grid 0 01 s DFT grid points 23506 979 points atom Setting up the DFT grid time to set the grid 0 03 s DFT grid points 65912 2746 points atom Start SCF Iterations Iter DIIS Error Energy change Electrons XC Energy Energy Time s gt gt gt Purifying P IDMP 1 53e 14 lt lt lt THRESPDP set to 1 00e 00 gt gt gt SWITCHING TO GRID 1 lt lt lt ele 0 3143222065 677 4535764850 01 9995043389 89 9757230998 677 4535764850 0 66 gt gt gt SWITCHING TO GRID 0 lt lt lt 2 0 6986364323 6 5996837687 01 9970678470 93 6280083063 670 8538927162 0 41 3 0 2864124356 8 2488710461 01 9980922169 93 2210986394 679 1027637623 0 39 4 0 1098582343 0 9402443640 01 9979502441 91 5162309843 680 0430081263 0 41 5 0 1379180296 0 0258751155 01 9976743328 92 0184706858 680 0688832418 0 40 6 0 0299984056 0 1205332226 01 9979006529 92 0222388541 680 1894164644 0 40 7 0 0073251834 0 0131962993 01 9978758774 91 9713249086 680 2026127637 0 39 gt gt gt SWITCHING TO GRID 1 lt lt lt 8 0 0036533335 0 0012610982 01 9996482881 91 9600999713 680 2038738619 0 67
25. h orbital one for the positive isosurface and one for the negative isosurface After adjusting the atomic representation create a new one and select orbital in the Drawing Method menu All MO s will be listed in the Orbital dropdown along with the orbital energy The Isovalue scroll bar controls the isosurface value in a u TeraChem User s Guide Page 20 2009 2012 PetaChem LLC TeraChem User s Guide W Graphical Representatio Selected Molecule talslog Create Rep Delete Rep Style Color Selection CPK Name all Orbital ColorlD O all Selected Atorns fan Draw style Selections Trajectory Periodic Coloring Method Material h Drawing Method ESE n Range Hz 1 Orbital 752 Ene y Isovalue Eoo fF Step Wi Go y Draw Solid 5 Size dl Ga 9 show isosurface v Apply Changes Automatically Apply CO lol x File Molecule Graphics Display Mouse Extensions Help ID T A D F Molecule Atoms Frames Vol 3 TAD orbitals log 24 10 0 9 4 41 zoom E I Y step 1 H speed 1D Figure 2 Caffeine molecule orbitals output orbitals log in VMD TeraChem User s Guide Page 21 2009 2012 PetaChem LLC VI Interactive calculations Interactive calculations are especially suitable for remote jobs when TeraChem is running on a remote machine cluster and the traje
26. hank Nathan Luehr for contribution of the GPU accelerated code for construction of numerical DFT grids and Alexey Titov for contribution of GPU accelerated code for electron repulsion integrals involving d functions Geometry optimization and transition state search calculations use the DL FIND library created by Johannes K stner at Stuttgart University Hartree Fock and DFT dispersion correction code is used with permission from Stefan Grimme at the University of M nster TeraChem uses standard Gaussian basis sets available at EMSL website http www emsl pnl gov forms basisform html TeraChem User s Guide Page 4 O 2009 2012 PetaChem LLC Il Getting started System requirements This version of TeraChem was compiled and tested under 64 bit RedHat Enterprise Linux 5 5 operating system running on Intel Core2 quad core and Intel Xeon 5520 dual quad core CPU machines An Nvidia compute capability 2 0 Tesla C2050 or similar or higher i e Tesla K20 or similar graphics card is required to run the program Please refer to the CUDA Programming Guide at http www nvidia com object cuda develop html for the most current list of Nvidia GPU s that meet this requirement A CUDA driver 304 54 or later must be installed on the system as well as v5 0 of the CUDA Toolkit Note that other CUDA toolkits even newer versions are not guaranteed to run correctly and will likely fail Details on how to obtain and install the CUDA driver are provided below
27. his file name can be modified by the orbitals parameter Because the orbitals require much disk space they can be written every n MD step specified by orbitalswrtfrq The orbitals can be visualized by VMD Note that the only meaningful information contained in this file is the MO coefficients Everything else is printed for VMD to parse the file correctly scr molden mo1f the canonical MO orbitals in Molden format scr charge x1s a tab separated file containing Mulliken atomic charges scr oe xls MO energies Geometry Optimization Transition State Search scr optlog xls a tab separated file containing 7 columns of which only one the first one is currently used The first column contains the SCF energy during geometry optimization or transition state search scr optim xyz geometry optimization or transition state search depending on the job type trajectory file in the XMol format The trajectory can be visualized by VMD Transition State Search scr neb n xyz an XMol file containing trajectory of the n NEB image The last image i e the neb_10 xyz ifmin_ image equals 10 is the actual transition state that that is also stored in optim xyz file scr nebinfo contains energies of all min image 1 NEB images along the converged NEB path scr nebpath xyz contains XYZ coordinates of all min image 1 NEB images along the converged NEB path MD simulation scr log xls a tab separated file contai
28. ify the number of atoms subject to steering forces the identity of the atoms which are being steered the fixed in Cartesian space points they are being pulled toward and the magnitude of the force This is accomplished with the steering file located in the same directory as the input file which has the following format Number Steered Atoms Steered Atom _ Index Fixed Point X Fixed Point Y Fixed Point _Z Steering Force where the last line occurs Number _Steered_ Atoms times Coordinates of the fixed points should be given in bohr and the steering force should be given in atomic units Output files In addition to the information displayed on the screen TeraChem creates several output files All calculations M T Ong J Leiding H Tao A M Virshup and T J Martinez J Amer Chem Soc 131 6377 2009 TeraChem User s Guide Page 12 2009 2012 PetaChem LLC TeraChem User s Guide scr c0 scr ca and scr cb in UHF and UKS jobs the converged WF binary file containing the MO coefficients C i 3 where i row is the MO and j column is the AO basis function index This file can be used as initial WF guess in subsequent calculations scr prjct scr prjcta and scr prjctb in UHF and UKS jobs the converged WF projected onto another usually larger basis set These files are generated by project jobs and used as an efficient initial guess scr orbitals log the canonical MO orbitals in GAMESS format T
29. ile Here is an example coordinates file for a hydrogen molecule TeraChem User s Guide Page 9 O 2009 2012 PetaChem LLC TeraChem User s Guide 2 Hydrogen Molecul Xmol format H 0 0 0 0 0 0 H 0 7 0 0 0 0 Some jobs for example transition state search using NEB method require several sets of coordinates frames In this case all frames should be listed in the coordinates file one by one i e 2 Hydrogen Molecul Xmol format frame 1 H 0 0 0 0 0 0 H 0 7 0 0 0 0 2 Hydrogen Molecul Xmol format frame 2 H 0 0 0 0 0 0 H 0 8 0 0 0 0 Note that there should be no blank lines between individual frames The PDB format often used for protein molecules is also supported and will be automatically assumed if the filename for the coordinates ends in pdb More details on PDB file format are available at http www wwpdb org docs html Basis set file format TeraChem supports standard atom centered Gaussian type basis sets such as those available at EMSL website http www emsl pnl gov forms basisform html The basis set information used by TeraChem is provided by a set of files in basis directory This directory should be located as STeraChem basis where the environment variable TeraChem is set to the TeraChem installation directory by default All basis sets are listed in individual files For every atom in a basis set the first four lines specify the atom type number of core orbitals number of valence
30. ion conventional Force conventional Fock matrix formation auto Use conventional algorithm if diffuse basis functions are detected or incremental otherwise auto maxit Maximum number of SCF iterations integer 100 convthre WF convergence threshold float 3 0e 5 threall Two electron integral threshold float Two electron integrals less than this threshold are neglected 1971 xtol Basis set linear dependency threshold float When diffuse basis functions are used xtol and convthre may need to be raised up to 1 0e 3 1 0e 4 dispersion dftd alias Should empirical dispersion corrections be used yes no d3 d2 D2 and D3 are two different dispersion parameterizations developed by S Grimme units Units used for coordinates angstrom or bohr angstrom nbo NBO analysis no yes npa full advanced nbo no no NBO analysis yes npa Natural population analysis only full Full NPA NBO analysis advanced nbo Analysis with NBO input TeraChem uses v6 0 of the NBO package See www chem wisc edu nbo5 for documentation of the earlier v5 0 no polarizability Calculate polarizability tensor yes no no safemode Allow to pre configure GPUs for basis sets with d functions Setting this parameter to no bypasses pre configuration step but allows to have more GPU yes 1 A M N Niklasson Phys Rev
31. it is on grid 0 is used to converge the wavefunction until the DIIS error reaches the gridthre value default 0 01 Grid dftgrid is then used to finally converge the wavefunction yes gridthre Threshold for switching dynamical DFT grids guess generate Or path to the WFfile generate means the initial WF guess is generated from scratch using maximum orbital overlap otherwise it is loaded from the WF file The WF is dumped in the end of each calculation to the scr c0 file scr ca scr cb in unrestricted methods To load WF in unrestriced calculations guess requires two parameters for example guess scr ca scr cb generate scf diis Use Pulay s DIIS for SCF convergence oda Use optimal damping for SCF convergence diis a Hybrid DIIS A DIIS scheme diis prime DIIS with density matrix purification instead of diagonalization can be faster when there are more than 3000 basis functions diis J M Langlois et al J Phys Chem 98 13498 1994 7 P Pulay J Comp Chem 3 556 1982 E Cances and C Le Bris Int J Quantum Chem 79 82 2000 X Hu and W Yang J Chem Phys 132 054109 2010 TeraChem User s Guide Page 25 2009 2012 PetaChem LLC TeraChem User s Guide start _diis When using optimal damping switch to DIIS once DIIS error falls below threshold float fock incremental Force incremental Fock matrix format
32. k All suggestions comments or other feedback concerning your experience with or use of the Software that may be given to PetaChem Feedback will be given voluntarily and without obligation or restriction of any kind PetaChem may use such feedback for any purpose Due to the nature of development work PetaChem will not commit to correcting any reported errors or discrepancies Feedback will not create any confidentiality obligation for PetaChem You will not give Feedback that is subject to license terms that seek to require any product technology or service that incorporates or is derived from Feedback or any intellectual property to be licensed to or otherwise shared with you or any third party 7 Disclaimers of Warranty and Liability a TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW PETACHEM PROVIDES THE SOFTWARE AS IS AND WITH ALL FAULTS PETACHEM HEREBY DISCLAIMS ALL EXPRESS IMPLIED OR STATUTORY REPRESENTATIONS WARRANTIES AND CONDITIONS REGARDING THE SOFTWARE INCLUDING BUT NOT LIMITED TO MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE TITLE QUIET ENJOYMENT OR NONINFRINGEMENT THE ENTIRE RISK AS TO THE QUALITY OF THE SOFTWARE ITS USE OR PERFORMANCE REMAINS WITH YOU b IN NO EVENT WILL PETACHEM BE LIABLE FOR ANY LOSS OR DAMAGE INCLUDING WITHOUT LIMITATION ANY SPECIAL INCIDENTAL INDIRECT SPECIAL OR CONSEQUENTIAL LOSS OR DAMAGE WHATSOEVER WHETHER FOR BREACH OF CONTRACT IN NEGLIGENCE OR ON ANY OTHER THEORY OF LIA
33. l cuda 5 0 1ib64 libcufft so 5 0 0x00007fe60c656000 libcuda so 1 gt usr lib64 libcuda so 1 0x00007fe60ba6 000 libm so 6 gt lib64 libm so 6 0x000000382dc00000 libstdc so 6 gt usr lib64 libstdc so 6 0x000000383ce00000 libgcc_s so 1 gt 1ib64 libgcc_s so 1 0x0000003839600000 libc so 6 gt 1ib64 libc so 6 0x000000382d800000 1ib64 1d linux x86 64 s0 2 0x000000382c400000 libdl so 2 gt 1ib64 libdl so 2 0x000000382e000000 librt so 1 gt 1ib64 librt so 1 0x000000382 400000 libz so 1 gt lib64 libz so 1 0x00000034c0a00000 libcublas so 5 0 gt usr local cuda 5 0 1ib64 libcublas so 5 0 0x00007fe60e65c000 libcudart so 5 0 gt usr local cuda 5 0 1ib64 libcudart so 5 0 0x00007fe60b815000 HAE a AAA AAA KARA KARA RARA License Check k kk ik k k kk kk kk k k Use license from home ufimtsev petachem TeraChem license dat Available Host id 003048DA94D0 Available Host id 003048DA94D1 Available Host id 3243CCBF8B03 License expires 2013 01 05 KKKKKKK KK KKK KKK KK KK KKK License OK KKKKKKK KKK KKK KKK KKK KK KK KK Scratch directory scr XYZ coordinates caffeine xyz Using basis set 6 31gs Spin multiplicity 1 Using DIIS algorithm to converge WF WF convergence threshold 3 00e 05 Maximum number of SCF iterations 100 Incremental Fock matrix formation Will switch to conventional Fock is diffuse functions are detected PRECISION DYNAMIC X matrix tolerance
34. l send you a permanent license file which should be saved as license dat in the TeraChem installation directory TeraChem environment variable indicates where the licensing file can be found i e TeraChem license dat Running sample jobs TeraChem package contains several sample jobs located at instdir TeraChem terachem tests After installation ca to the caffeine directory and run TeraChem by typing source instdir TeraChem SetTCVars sh instdir TeraChem terachem start sp where instdir is the installation directory you chose during the install defaults to your home directory and start sp is the name of a TeraChem input file Note that the environment variable TeraChem is set by source ing SetTCVars sh This is needed in order for TeraChem to locate the license and basis set library files The start sp contains the required parameters of the job including the filename of the file which contains the atomic coordinates for the molecule of interest Most of the parameters have default values The complete list of parameters available in this version is presented in Table 1 An example of the configuration file used for single point energy calculations of caffeine with the BLYP functional DFT D dispersion corrections and the 6 31G basis set is TeraChem User s Guide Page 6 O 2009 2012 PetaChem LLC TeraChem User s Guide Job Single point energy of caffeine basis set basis 6 31g coordinates file coor
35. matrix fischer almlof chemically motivated guess Hessian usually the best choice min_delta Atomic displacement in finite difference calculations 0 003 min_max_step Maximum step size in internal coordinates 0 5 min_restart Whether the optimization TS search job is started from scratch no or loaded from the checkpoint files no yes TeraChem User s Guide Page 27 2009 2012 PetaChem LLC TeraChem User s Guide min dump How often the checkpoint files are written By default at each 10 step 10 ts_method Transition state search method neb_free neb_restricted neb frozen neb free cart neb restricted cart neb frozen cart neb _ free Nudged Elastic Band NEB with free endpoints neb restricted NEB with endpoints allowed to move perpendicularly to their tangent direction neb_ frozen NEB with frozen endpoints neb x cart only initialization is performed in min coordinates coordinates while the TS search is done in Cartesians neb free min image Number of NEB images in the TS search calculations Should be greater than one The images are listed in the input coordinates file specified by coordinates If the number of images found is smaller than min image the program will automatically generate missing images by interpolation At least two images endpoints should be listed in the coordinates file The last one i e the min image
36. ning 7 columns 1 SCF energy 2 currently not in use 3 Kinetic energy 4 Temperature 5 Total energy SCF Kinetic 6 HOMO energy 7 LUMO energy All energies are in Hartree and the temperature is in degrees Kelvin In NVT dynamics the Total energy does not include the contribution from the damping force and thus should not be conserved scr coors xyz the MD trajectory geometry file in the XMol format The trajectory can be visualized by VMD TeraChem User s Guide Page 13 2009 2012 PetaChem LLC TeraChem User s Guide scr vel log contains atomic velocities along in the MD trajectory The format is similar to that of scr coors xyz except there is a blank line separating each set of velocities scr restart md a binary MD restart file containing all information wavefunction coordinates velocities etc required to restart an MD job By default this information is stored at every 100 MD iteration A user can change it by specifying restartmafreq parameter in the start file TeraChem User s Guide Page 14 2009 2012 PetaChem LLC IV More details on some TeraChem capabilities Wavefunction projection Sometimes especially when transition metals or diffuse basis functions are present in a system the SCF procedure does not converge due to insufficiently accurate initial guess In such cases it often helps to converge the wavefunction using a smaller basis set mini sto 3g etc with no diffuse functions
37. orbitals and the total number of contracted basis functions centered on the atom Consider an iron atom in STO 3G basis set ATOM Fe COR 9 VAL 4 BFS 19 Here Fe is an alias of the atomic nuclear charge z and Brs is the total number of atomic shells multiplied by the number of basis functions per shell 1 for s 3 for P 6 for D she11 etc The next block contains coefficients of atomic orbitals AOs that need to be precalculated separately for each atom and each basis set Below are 2 out of 13 AOs of iron in STO 3G basis set Oe 0 0 0 Booo 92667130e 01 00000000e 00 00000000e 00 00000000e 00 00000000e 00 00000000e 00 00000000e 00 39883475e 01 93498346e 02 00000000e 00 00000000e 00 90570755e 03 Lu 0 0 90570755e 03 55903797e 02 00000000e 00 00000000e 00 i 0 0 Die 99232061e 04 00000000e 00 00000000e 00 90570755e 03 00000000e 00 00000000e 00 00000000e 00 02744686e 02 00000000e 00 00000000e 00 00000000e 00 88180817e 01 44836578e 11 00000000e 00 06687307e 01 98455286e 01 0 0 0 00000000e 00 00000000e 00 00000000e 00 00000000e 00 00000000e 00 83366410e 01 This information is required to construct the initial guess as described in TeraChem User s Guide Page 10 2009 2012 PetaChem LLC TeraChem User s Guide J M Langlois T Yamasaki R P Muller and W A Goddard III Rule Based Wave Function for Generalized Valen
38. rames one by one In geometry optimization jobs only the first frame is taken into account while the others if any are ignored The second frame gt S F Boys and F Bernardi Mol Phys 19 552 566 1970 TeraChem User s Guide Page 17 O 2009 2012 PetaChem LLC TeraChem User s Guide however is required by transition state search jobs and represents the second NEB endpoint in NEB calculations The TS search is triggered by the ts keyword i e file start ts basis set basis 6 31g coordinates file coordinates sp xyz molecule charge charge 0 SCF method rhf blyp b3lyp etc RHF method ERE type of the job energy gradient md minimize ts TS search run ts end Sconstraints Send group in the configuration file allows one to impose geometrical constraints during optimization frozen atoms fixed bond lengths angles and dihedrals instdir tests constraints directory contains two example start files for constrained geometry optimization jobs Constrained geometry optimization can be performed in any type of coordinates with two exceptions 1 if DLC coordinates are used for optimization the default no atoms may be frozen and 2 if Cartesian coordinates are used for optimization min coordinates cartesian only frozen atom constraints are allowed Below is an example of a job configuration start file Note that all constraints should be listed in separate lines and enumeration of atoms begins from 1
39. rtial copies thereof b Copy modify or create derivative works of the Software in any way c Remove any copyright notice or licensing information contained in the Software d Disassemble or otherwise reverse compile or reverse engineer the Software or e Install the Software on any computer which is not a Licensed Computer Copyright All content included in the Software including without limitation text graphics images logos audio or video clips digital downloads data compilations is the property of PetaChem or licensors and protected by the laws of the United States and other countries and international treaties All trademarks that are not owned by PetaChem that appear in the Software are the property of their respective owners which may or may not be affiliated with or connected to PetaChem Any reports or published results obtained with the Software will acknowledge its use by appropriate citation as follows TeraChem v 1 5 PetaChem LLC 2011 See http www petachem com TeraChem User s Guide Any published work which utilizes TeraChem shall include the following reference I S Ufimtsev and T J Mart nez Quantum Chemistry on Graphica Processing Units 3 Analytical Energy Gradients and First Principles Molecular Dynamics Journal of Chemical Theory and Computation 5 2619 2628 2009 Electronic documents will include a direct link to the official TeraChem page at http www petachem com 6 Feedbac
40. t and they will be modeled using the TIP3P force field One signals that a QM MM calculation is desired by including the qmmm keyword in inputfile The keyword specifies the location of a file with coordinates for the desired MM water molecules Note that the coordinates of the MM waters are not in the coordinates file The water molecule positions must appear in a specific order grouped by water molecule and in the order O H H We provide an example for one QM water molecule surrounded by one MM water molecule inputfile TeraChem User s Guide basis 6 31lg qmmm mmwater xyz coordinates qmwater xyz run minimize end qmwater xyz 3 O 6 144353 0 788526 6 483525 H 6 378922 1 564817 5 989856 H 6 475062 0 043630 5 995619 mmwater XyZ 3 O 6 450776 0 962914 3 536427 H 6 338156 15 5LA3 5 5 2 771897 H 6 519847 1 524502 4 303300 It is also possible to use TeraChem with Amber 12 for more involved QM MM calculations e g where the MM region includes protein residues See the Amber 12 manual for details Integration with NBO6 This release of TeraChem is interfaced with the NBO6 package of Weinhold and coworkers NBO deletions are not currently supported nor are analyses which require the matrix elements of the dipole operator However many of the usual natural bond orbital NBO and natural population analyses NPA are supported Setting the nbo keyword in the startfile to npa or full will give natural population anal
41. t and warrant that you are not located in any such country or on any such list You also agree that you will not use the Software for any purpose prohibited by United States law including without limitation the development design manufacture or production of nuclear missiles or chemical or biological weapons 9 Miscellaneous a C d This Agreement will be governed by and construed in accordance with the laws of the State of California as if entered into and performed wholly within the state and without regard to the principles of conflicts of law You consent to exclusive jurisdiction and venue in the courts within the Northern District of California This Agreement constitutes the entire agreement between parties with respect to the Software and merges all prior and contemporaneous communications If any provision of this Agreement is held to be void or unenforceable for any reason that provision will be enforced to the maximum extent permissible so as to effect the economic benefits and intent of the parties and the remaining provisions of this Agreement shall remain in full force and effect Neither party s failure or delay in exercising any of its rights will constitute a waiver of such rights Any waiver or amendment of any provision of this Agreement will be effective only if in writing and signed by authorized representatives of both parties Neither party may represent or bind the other in any way and nothing in this
42. taChem hereby grants you a limited nonexclusive and nontransferable license to use in binary form one 1 copy of the Software and any updates patches enhancements technical support documentation and any related materials provided by PetaChem collectively Software You may install and use the Software on one computer with up to eight central processing unit cores and eight graphical processing unit cards the Licensed Computer The Licensed Computer may be a storage device such as a network server used only to install or access the Software from other computers over an internal network provided that each separate computer which accesses or uses the Software is a Licensed Computer License Termination This license and Agreement is effective until terminated This Agreement will terminate with or without notice on any breach by you of this Agreement You may terminate this Agreement at any time Promptly upon termination you will cease using and destroy all copies of the Software in your possession or under your control Sections 3 9 of this Agreement will survive any termination of this Agreement License Limitations The Software is licensed and not sold All rights not expressly granted herein are reserved by PetaChem Except as expressly authorized in this Agreement you will not a Sell rent lease distribute sublicense assign publish or otherwise transfer including by loan or gift the Software or any full or pa
43. ux operating system Some of TeraChem features include Restricted unrestricted and restricted open shell Hartree Fock and grid based Kohn Sham energy and gradient calculations Full support of s p and d type atom centered Gaussian basis functions Various DFT functionals including range corrected and Coulomb attenuated functionals BLYP B3LYP PBE PBEO PBE PBEh 0B97 0B97x camB3LYP etc and DFT grids 800 80 000 grid points per atom o Static grid single grid used for the entire calculation and dynamical grid multigrid integration o Empirical dispersion correction DFT D3 and DFT D2 Geometry optimization L BFGS Conjugate gradient Steepest descent o The optimization can be carried out either in Cartesian or internal coordinates as specified in the start file all input geometries are provided in Cartesians The Cartesian internal gt Cartesian coordinate transformation is performed automatically whenever required o Constrained optimization with frozen atoms constrained bond lengths angles and dihedrals Transition state search Nudged elastic band in internal and Cartesian coordinates Ab initio molecular dynamics NVE NVT ensembles o Reversible Born Oppenheimer dynamics o Spherical boundary conditions Support of multiple GPU systems Single Dynamical Double precision accuracy QM MM treatment of surrounding water molecules using TIP3P force field Natural bond orbital analysis through integration
44. with NBO6 Polarizabilities for HF and closed shell DFT methods See Table 1 for a complete list of TeraChem capabilities W L Jorgensen J Chandrasekha J D Madura R W Impey and M L Klein J Chem Phys 79 926 1983 TeraChem User s Guide Obtaining TeraChem To purchase a copy of TeraChem visit http shop petachem com Pricing information is available at http www petachem com pricing html Citing TeraChem Any published work that utilizes TeraChem shall include the following reference I S Ufimtsev and T J Martinez Quantum Chemistry on Graphical Processing Units 3 Analytical Energy Gradients and First Principles Molecular Dynamics J Chem Theory Comput 2009 5 p2619 Work which uses the geometry optimization or transition state finding utilities shall include the following reference J Kastner J M Carr T W Keal W Thiel A Wander and P Sherwood DL FIND An Open Source Geometry Optimizer for Atomistic Simulations J Phys Chem A 2009 113 p11856 Whenever dispersion corrections are used the following references should be cited S Grimme J Antony S Ehrlich and H Krieg J Chem Phys 2010 132 p154104 S Grimme S Ehrlich and L Goerigk J Comput Chem 2011 32 p1456 Acknowledgements This software was developed by Ivan Ufimtsev and Todd Martinez at the University of Illinois at Urbana Champaign and PetaChem LLC The authors would like to especially t
45. ysis or full NBO NPA analysis You may also use advanced keywords documented in the NBO manual if desired In this case the nbo keyword should be set to advanced and the startfile should contain a Snbo group as documented in the NBO manual An example of this usage of advanced keywords for CH3NH is provided in TeraChem tests nbo Note that the NBOEXE environment variable needs to point to the NBO6 executable file in order for successful integration with TeraChem This is currently set in the SetTCVars sh script The NBO6 executable is included with the TeraChem distribution and resides in the TeraChem directory Ghost Atoms Sometimes it is desirable to do calculations including the basis functions of an atom or atoms without including the nucleus or electrons corresponding to the atom This is most often used to http ambermd org http www chem wisc edu nbo5 TeraChem User s Guide Page 16 2009 2012 PetaChem LLC TeraChem User s Guide calculate basis set superposition error BSSE For example the Boys Bernardi counterpoise correction for the interaction energy of fragments A and B is Eyer E Hip Ri Rp AU B E H R 3AU B E H R AUB where the first arguments in the parentheses are the Hamiltonian and coordinates it depends on and the second arguments after the semicolon are the basis sets used Thus in the second term on the right the calculation has the atoms of A and the corresponding basis functions
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