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. 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 the charge.

A LOT

Specify multiplicity.

SCFTYP

Specify SCF calculation method.

RUNTYP

Select the calculation purpose.

COORD

Specify the format of molecular structure data.

MAXIT

Specify the upper limit of the SCF calculation iteration number.

NZVAR

Specify the number of internal coordinates.

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)

ECP

Specify Pseudopotential.

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

Others

Fill in other keywords.

$BASIS

Basis Set

Select the basis function system. It is reflected in GBASIS, NGAUSS, NDFUNC, NFFUNC, DIFFSP, DIFFS.

GBASIS

Basic set of basis functions

NGAUSS

Number of Gaussian functions

EXTFIL

Read the basis function from an external file.

NDFUNC

Number of added d-polarization functions

NFFUNC

Number of added f-polarization functions

NPFUNC

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

Calculation time limit (default 600 minutes)

MWORDS

Memory usage (default 1 MW)

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.

Others

Fill in other keywords.

Z-Matrix

Make Z-Matrix settings.

DFT

$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)

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.

6.7.2. Import Keywords¶

Only keywords (calculation conditions) are read from the existing GAMESS input file.

6.7.3. Import from Punch File¶

6.7.3.1. Import $VEC¶

Import $VEC from the punch file.

6.7.3.2. Import $HESS¶

Import $HESS from the punch 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, output format of coordinates changes according to the selection of Coordinate Format choice (Z-Matrix or XYZ) and Z-Matrix / XYZ tab of Coordinate Viewer.

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. 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 window.

6.7.7. Analyses¶

6.7.7.1. MO, UV-Vis, Charge & NMR¶

Obtain information on molecular orbital, UV-Vis, charge, NMR from theout file information and display it.

Information on the charge read can be displayed in Viewport by selecting View ‣ Labels/Charges ‣ Show Mulliken Charge and so on.

Refer to Energy Level Diagram window, MO Plot window, UV-Vis Spectrum window, NMR Window for how to operate the subwindow.

6.7.7.2. IR/Raman¶

Select the out file and display the vibration spectrum (IR or Raman spectrum).

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.

6.7.7.3. 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.

Warning

To use this function, CygwinWM setup is required.

6.7.8. PDB¶

6.7.8.1. Edit PDB File¶

Editing of atom deletion etc. is done while leaving residue information etc. of PDB data etc.

6.7.8.2. FMOutil¶

Start FMOutil.

6.7.9. Paired Interacting Orbitals¶

Paired Interacting Orbitals Executes analysis. For details, see PIO analysis window.