6.7. QM ‣ GAMESS 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

Set up and run the GAMESS calculation flow in project mode.

Preset

Import and saves a preset of settings.

# of Jobs

Specify the number of jobs.

Import

Import the settings output by Export. Click the arrow to the right of the button to recall settings used in the past.

Export

Output settings to file.

OK

Run a calculation or generate a file with your settings.

Details

Set up detailed calculation conditions. The Configure will be launched.

Task

Specifies the type of calculation.


Setting details
Optimize
RUNTYP=OPTIMIZE
Energy
RUNTYP=ENERGY
IR
RUNTYP=HESSIAN
Raman
RUNTYP=RAMAN
TDDFT
RUNTYP=ENERGY
TDDFT=EXCITE
Optimize(TS)
RUNTYP=SADPOINT
Optimize(TDDFT)
RUNTYP=OPTIMIZE
TDDFT=EXCITE
RESP
RUNTYP=ENERGY
Add setting to $CONTRL’s Others
Add setting to Others
IRC(Forward)
RUNTYP=IRC
IRC=True
FORWRD=True
IRC(Reverse)
RUNTYP=IRC
IRC=True
Optimize+IR
RUNTYP=OPTIMIZE
HSSEND=True
Optimize(TS)+IR
RUNTYP=SADPOINT
HSSEND=True
Method

Specify calculation method.


Setting details
CCSD
CCTYP=CCSD
CIS
CITYP=CIS
Basis set

Specify a default 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 Save as Default ‣ Clear Default Settings.

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.

Difference between Run (1) GAMESS and Run (2) GAMESS is the program path of GAMESS to start. You can change the program path with Tools ‣ Preferences ‣ Program Path. Run (1) GAMESS, Run (2) GAMESS is supposed to set Firefly or GAMESS of different versions etc. and use them while using them according to the scene It is.

To use the external basis function file (: command: $ BASIS EXTFIL = .T.), Put basis.lib in 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.inp is also shown.

type

Description

out file
water.out

Calculation log file.

bat file
water.inp.bat

This is a batch file for running GAMESS.

pun file
water.pun
It is a punch file for detailed result analysis.

The 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 View ‣ Labels/Charges ‣ Show Mulliken Charge and so on.

See Energy Level Diagram window , Surface Setup 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 Preference ‣ Easy Setup. 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.