6.7. menu
It is a menu related to GAMESS.
In order to use GAMESS you need to install GAMESS separately. The way to install GAMESS is described in Installing Winmostar and solvers.
6.7.1. Workflow Setup
Sets up and executes the GAMESS calculation flow in project mode. Local jobs in project mode will use the binary specified in GAMESS(1) in .
- Preset
Import and saves a preset of settings.
- # of Jobs
Specify the number of jobs.
- Enable parameter/structure scan
This feature requires the purchase of an add-on. It allows you to run multiple calculations where only certain parameters differ (parameter scan) or to run calculations with the same parameters for multiple structures (structure scan).
Click Config to open the configuration window for the scan calculation. For parameter scans, select %WM_SCAN1% for the Target Variable and enter the parameters you wish to set for %WM_SCAN1% in each row of the Values. Then, enter %WM_SCAN1% in the parameters you want to set in the Workflow Settings window or Keyword Settings window. For structure scan, select %WM_STRUCT% for Target Variable when the animation appears in the molecule display area (e.g., by opening an SDF file).
After the scan calculation is finished, use to tabulate the calculation results.
- Import
Import the settings output by Export. Click the arrow to the right of the button to recall settings used in the past on the same project or Winmostar.
- Export
Output settings to file.
- OK
Run a calculation or generate a file with your settings. See For project mode for details.
- Details
Set up detailed calculation conditions. The Configure will be launched.
- Task
Specifies the type of calculation. Keywords without a group name beginning with $ are from $CONTRL.
- Method
Specifies the calculation method (Hamiltonian). Keywords without a group name beginning with $ are from $CONTRL.
- Basis set
Specifies a basis function.
- Charge
Specify charge.
- Multiplicity
Specify spin multiplicity.
- Solvent
Specify PCM solvent type.
6.7.2. Configure
Set calculation conditions of GAMESS. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.
See the (1) Run GAMESS, (2) Run GAMESS for the behavior when clicking Run.
Return to the default state with Reset button. Save the current state as the default state with Save as Default button. Restore the default state to the factory condition with .
- Easy Setup
Shows the simple setting window.
- NCPUS
Specify the parallel number.
- NODES (FireFly)
Specify the directory of the node used for calculation.
- Basic Tab
- $CONTRL
- ICHARG
Specify charge.
- A LOT
Specify spin multiplicity.
- SCFTYP
Specify SCF calculation method.
- RUNTYP
Select the calculation purpose.
- COORD
Specifies the format of the molecular structure coordinates. It is linked to the $DATA coordinate format.
- MAXIT
Specify the upper limit of the SCF calculation iteration number.
- NZVAR
Specifies the number of internal coordinates. %NZVAR% is assigned 5000 if ZMAT contains DLC=.T. AUTO=.T., 3N-6 if RUNTYP=OPTIMIZE with IFREEZ and 1 numerator and 5 or more atoms, and 0 otherwise.
- EXETYP
To specify whether or not to actually perform the calculation, specify CHECK to check the input.
- NOSYM
Specify whether to use symmetry in calculation.
- NPRINT
Specify the detail level of the output.
- LOCAL
Specify the method of localization of the trajectory. (Default 0 = not)
- PP
Specify Pseudopotential (Effective Core Potential, ECP).
- DFTTYP
Specify the basis function system of the density functional theory method.
- TDDFT
Specify whether energy calculation of excited state is performed using time-dependent DFT method
- CITYP
Specify whether to perform placement interaction (CI) calculations.
- CCTYP
Specify whether or not to perform combined cluster (CC) calculations.
- ISPHER
Specifies whether the basis functions should be treated as Cartesian or spherical harmonic functions. (Default -1 = Cartesian)
- MPLEVL
Specify whether to perform Moller-Plesset perturbation (MP) calculations.
- Others
Fill in other keywords.
- $BASIS
- Basis Set
Specifies the base function system, reflected in GBASIS, NGAUSS, NDFUNC, NFFUNC, DIFFSP, and DIFFS.
- GBASIS
Specify the base set of the base function system.
- NGAUSS
Specify the number of Gaussian functions
- EXTFIL
Read the basis function from an external file.
- NDFUNC
Specify the number of added d-polarization functions
- NFFUNC
Specify the number of added f-polarization functions
- NPFUNC
Specify the number of added p-polarization function
- DIFFSP
Specify whether to add sp-diffuse function
- DIFFS
Specify whether to add s-diffuse function
- Others
Fill in other keywords.
- Advanced tab
- $SYSTEM
- timl
Specify calculation time limit (default 525600 minutes)
- MWORDS
Specify memory usage (default 1 MW)
- MEMDDI
Specify maximum summed memory usage for DDI. (Default 1MW)
- Others
Fill in other keywords.
- $SCF
- DIRSCF
Specify whether to use direct SCF calculation method.
- DAMP
We use Davidson damping to create Fock matrix.
- CONV
Specify the threshold of density change at SCF convergence judgment. (Default 1.0D - 05)
- Others
Fill in other keywords.
- $GUESS
- GUESS
Specify how to calculate the initial wave function.
- Others
Fill in other keywords.
- $STATPT
- NSTEP
Specify the upper limit of the number of steps of structure optimization. (Default 20)
- OPTTOL
Specify the threshold of the energy gradient. (Default 0.0001 Hartree/Bohr)
- METHOD
Specify algorithm for structure optimization.
- HESS
Specify how to obtain the Hessian matrix.
- HSSEND
Specifies whether or not a Hessian matrix is desired at the end of the calculation.
- Others
Fill in other keywords.
- $FORCE
- TEMP
Specifies the temperature (Kelvin) in thermodynamic data calculations. (default 298.15)
- Others
Fill in other keywords.
- Z-Matrix tab
- Set “DLC=.T. AUTO=.T.” if RUNTYP=OPTIMIZE, (# atoms)>5 & (# mols)=1
If checked, set %ZMATDLC%. Set %ZMATDLC% to “DLC=.T. AUTO=.T.” if RUNTYP=OPTIMIZE without IFREEZ and with 1 numerator and 5 or more atoms.
- DFT tab
- $DFT
- LC
Specify whether to perform long distance correction. (Only for BLYP, BOP and BVWN)
- MU
Specify the value of long-distance correction parameter. (Default 0.33)
- DC
Specifies whether Grimme’s empirical dispersion force correction should be applied.
- IDCVER
Specifies the version of Grimme’s empirical dispersion force correction.
- Others
Fill in other keywords.
- $TDDFT
- NSTATE
Specify the number of desired states (excluding the base state).
- NRAD
Specify the number of grid points in the radial direction for deriving the derivative of density functional. (Default 48)
- NLEB
Specify the number of lattice points in the angular direction. (Default 110)
- Others
Fill in other keywords.
- MP2 tab
- $MP2
- CODE
Specify the directory of the node used for calculation.
- Others
Fill in other keywords.
- Solvent tab
- $PCM
- SOLVNT
Specify the solvent.
- SMD
Specify whether to use SMD (Solvent Model Density).
- IEF
Specifies the type of PCM model.
- ICAV
Specifies whether Cavitation energy should be calculated.
- TABS
Specify temperature (Kelvin). (default 298.0)
- Others
Fill in other keywords.
- $PCMCAV
- RADII
Specifies the type of cavity radius.
- Others
Fill in other keywords.
- IRC Tab
- $IRC
- FORWRD
Specifies forward or reverse direction.
- PACE
Specify IRC calculation method.
- NPOINT
Specify the number of IRC points.
- MXOPT
Specify the maximum number of steps for structural optimization at each IRC point.
- STRIDE
Specifies the distance between IRC points.
- SADDLE
Specifies whether the structure of $DATA is a saddle point.
- OPTTOL
Specifies the threshold value of the energy derivative to determine if a minimum point has been reached.
- Comment tab
Fill in your comments.
- Preview tab
A preview of the configuration keywords will be displayed.
- Import $HESS
Import $HESS from the punch file.
- Import $VEC
Import $VEC from the punch file.
- Reset
Reset settings.
- Import
Read the basis function from an external file.
- Export
Output configuration file.
6.7.3. Import Keywords
Only keywords (calculation conditions) are read from the existing GAMESS input file.
6.7.4. (1) Run GAMESS, (2) Run GAMESS
If the input file of GAMESS is opened in the main window, execute GAMESS using that file. If it is not open, save the input file of GAMESS and execute GAMESS.
When saving the input file, the atomic coordinate format of $DATA changes according to the setting of COORD in $CONTRL; for ZMTMPC, the format is MOPAC’s Z-matrix format, otherwise it is Cartesian format.
(1) GAMESS run , (2) GAMESS run are intended to be used with different versions of GAMESS, depending on the situation. The difference between (1) Execute GAMESS , (2) Execute GAMESS is the program path of GAMESS to be invoked. The program path used for each menu can be changed in .
To use the external basis function file (: command: $ BASIS EXTFIL = .T.), Put
basis.libin the same directory as GAMESS's EXE file. For WinGAMESS, specify setenv EXTBAS ../ basis.lib in :file:` runscript.csh`.Following file will be generated with execution. As an example, the file/folder name when the input file is
water.inpis also shown.
type
Description
water.outCalculation log file.
water.inp.batThis is a batch file for running GAMESS.
water.punThe job is run through Winmostar Job Manager.
6.7.5. Open Log File (out/log)
Open the out file with a text editor.
6.7.6. Show log excerpts
Excerpts of key information from the out file.
6.7.7. Animation(Optimization)
Create and display animation such as structure optimization, scanning, IRC calculation, etc. from the out file information.
For the animation display operation method, see Animation display area.
6.7.8. Analyses
6.7.8.1. Molecular Orbitals, Charge
Retrieve and display molecular orbital and charge information from out file information
Information on the charge read can be displayed in Viewport by selecting and so on.
See Energy Level Diagram window , Surface Setup / Cubgen window for subwindow operation.
6.7.8.2. UV-Vis Spectra
Displays UV-Vis spectra from information in out files.
See UV-Vis Spectrum window for subwindow operation.
6.7.8.3. NMR Spectra
Display NMR spectra from information in out file.
See NMR Window for subwindow operation.
6.7.8.4. IR/Raman
Display vibration spectra (IR or Raman spectra) from the information in the out file.
After loading the IR spectrum from the out file of RUNTYP = HESSIAN, if you subsequently read the out Raman spectrum of :command: RUNTYP = RAMAN in this menu, both spectra are displayed simultaneously in the subwindow can.
Refer to IR Spectrum Window for how to operate the subwindow.
6.7.8.5. RESP Charges
Calculate point charge based on RESP method from punch file.
The punch file to be loaded must be output from a calculation performed with the RESP/ESP setting selected in the . The spin multiplicity is treated with the assumption of 1.
After being asked “Do you assign the same charge to an atom that is structurally equivalent to a molecule?”, when you click Yes, it internally uses acpype, and when you click No, it internally uses AmberTools directly to calculate the RESP charge. Basically, it is recommended to click Yes, but in such cases, click No. It is expected that the results of both calculations will not change significantly. If you want to average the charges of structurally equivalent atoms (e.g. the three hydrogen atoms of a methyl group) after choosing No, use Average the group’s charge.
Note that Firefly is not supported by this feature.
Warning
To use this function, CygwinWM setup is required.
6.7.9. Edit PDB file
Editing of atom deletion etc. is done while leaving residue information etc. of PDB data etc.