6.8. QM ‣ Gaussian menu

It is a menu about Gaussian.

In order to use Gaussian you need to install Gaussian separately.

6.8.1. Configure

Set calculation conditions of Gaussian. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.

Behavior when clicking Run is see 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

Show the simple setting window.

%nprocshared

Specify the parallel number(Number of CPU cores used).

Link0

%Chk=file

Specify the checkpoint file.

%Mem=n

Specify the amount of dynamic memory in 8 bytes words. It is also possible to specify units of KB, MB, GB, KW, MB, GW. (Default: 800 MB)

Comment

Write a comment.

#

Specify the beginning of the route section.

#N

Output is done at the standard level. (Default)

#P

Perform detailed output. The execution time at the start and end of each link, and the information on convergence of SCF are output.

#T

Specify a concise output that only outputs important information and results.

Charge

Specify the value of the charge.

Multiplicity

Specify Spin multiplicity.

Additional Chg./Multi.

Specify additional charge and spin multiplicity.

Hamiltonian

Specify the Hamiltonian to use.

Ltd.

Perform Hartree-Fock calculation. Unless explicitly specified, RHF is used for singlet and UHF is used for higher multiplicity.

rhf

Restricted Hartree-Fock calculation is performed.

uhf

Unrestricted Hartree-Fock calculation is performed.

am1

We will perform semi-empirical calculations using AM1 Hamiltonian.

pm3

We perform semi-empirical calculation using PM3 Hamiltonian.

pm3mm

We perform semi-empirical calculations using PM3 Hamiltonian with molecular dynamics correction on HCON binding.

b3lyp

Compute the density functional method combining the Becke 3 functional with the LYP nonlocal correlation functional.

ub3lyp

Unrestricted version of b3lyp.

mp2

Following Hartree-Fock calculation, Moller-Plesset correlation energy correction up to the second order is performed.

ump2

It is an Unrestricted version of mp2.

mp4

Following Hartree-Fock calculation, Moller-Plesset correlation energy correction up to the fourth order is performed.

ump4

It is an Unrestricted version of mp4.

cis

Calculate the excited state using one-electron excitation CI.

cisd

Calculate the excited state using two electron excitation CI. (Synonymous with CI)

indo

We will perform semi empirical calculations using INDO Hamiltonian.

ondo

We will do semi-empirical calculations using CNDO Hamiltonian.

gvb

Perform general valence bond (GVB) calculation.

Basis

Specify the set of basis functions.

Pop

Control of molecular orbital output, electron density analysis, atomic charge distribution and so on.

none

It does not output molecular orbits and does not analyze electron density.

minimal

It outputs atomic charge and orbital energy.

regular

We output 5 occupied orbits and 5 virtual trajectories. Also output density matrix and Mulliken electron density analysis.

full

All occupied orbits and virtual trajectories are output. Also output density matrix and Mulliken electron density analysis.

mk

Output charge fitted to electrostatic potential in Merz-Singh-Kollman scheme.

chelp

Outputs charge fitted to electrostatic potential with CHelp scheme.

chelpg

Outputs charge fitted to electrostatic potential with CHelpG scheme.

(full,chelp)

Outputs charges fitted to the electrostatic potential in the CHelp scheme, all occupied orbitals and virtual orbitals. It also outputs the density matrix and Mulliken electron density analysis.

(fullchelpg)

Outputs charges fitted to the electrostatic potential in the CHelpG scheme, all occupied orbitals and virtual orbitals. It also outputs the density matrix and Mulliken electron density analysis.

(full,npa)

Outputs NBO (Natural Bond Orbital) charges by Natural Population Analysis, all occupied orbits and virtual orbits. It also outputs the density matrix and Mulliken electron density analysis.

OPT/IRC

Controls structural optimization or IRC calculations.

opt

Perform structure optimization.

opt=z-matrix

Structure optimization is performed with internal coordinates.

opt=modredundant

Add, delete, or modify the definition of redundant internal coordinates (including search and bound information). An input section is required after the structure specification.

opt=(ts,noeigentest,calcfc)

Optimize for transition state. We do not test curvature. Calculate the force constant for the first time.

opt=tight

Tighten the threshold for determining convergence of force and coordinate changes.

irc=(forward, maxpoint=20, stepsize=5, calcfc)

Tracks a forward reaction path. Specify the number of points on the path and the step size. Calculates force constants for the first time.

irc=(reverse, maxpoint=20, stepsize=5, calcfc)

Tracks the reaction path in the reverse direction. Specify the number of points on the path and the step size. Calculates force constants for the first time.

OptMaxCyc

Sets the maximum number of structural optimization steps.

Scrf

run the calculation with solvent effects.

SCF

Controls SCF calculations.

scf=tight

Convergence decision for normal SCF calculation. (Default)

scf=qc

Use second-order convergence method.

scf=xqc

If the first-order convergence method does not converge, switch to the second-order convergence method halfway through.

scf=vshift[=N]

Shifts orbit energy by N*0.001 Hartree, default value of N is 100.

Freq

Controls the calculation of force constants and frequencies.

freq

Calculate force constants and frequencies.

freq=raman

We calculate the Raman intensity in addition to the IR intensity.

freq=vcd

Calculate oscillating circular dichroism (VCD) intensity in addition to normal frequency analysis

freq = noraman

Hartree-Fock Raman intensity is not obtained by analytic frequency calculation.

freq=nraman

Calculate the polarizability derivative by numerically differentiating the analytical dipole derivative for the electric field.

freq=nnraman

Calculate the polarizability derivative by numerically differentiating the analytical polarizability on nuclear coordinates.

NMR

Controls NMR calculations.

nmr

Perform NMR calculations.

nmr=giao

Perform NMR calculations using the GIAO method. (Default)

nmr=csgt

NMR calculations using the CSGT method.

nmr=igaim

Perform NMR calculations using atomic center coordinates as gauge origin.

TD

for example,

Calculate excited state energies using the time-dependent Hartree-Fock or DFT method. (default singlet).

td=(nstates=n)

For the n states, we obtain the energy of the excited state using the time dependent calculation method. (Default 3)

td=50-50

Half of the states are calculated as singlet and the other half as triplet. Valid only for closed-shell systems.

td=triplets

Calculate the triplet state. Valid only for closed-shell systems.

EmpiricalDispersion

Enable empirical dispersion power.

pfd

Add Petersson-Frisch dispersion power.

gd2

Add D2 version of Grimme dispersion force.

gd3

Add D3 version of Grimme dispersion force.

gd3bj

Add D3 version of Grimme dispersion force with Becke-Johnson damping.

gfinput

Outputs the basis function system in the same format as the input format.

gfprint

It outputs the basis function system in tabular form.

nosymm

Do not reorient the coordinates, run the calculation with the input orientation.

guess=read

Read initial wave function from checkpoint file

geom=check

Fetch the molecule specification section from the checkpoint file.

Subsection

Fill in other keywords.

Coordinate format

Specifies the format of the atomic coordinates (Cartesian or Z-matrix).

Reset

Reset settings

Import

Output configuration file.

Export

Output the Cube file.

6.8.2. Import Keywords

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

6.8.3. Run

If Gaussian's input file is opened in the main window, use Gaussian to execute it. If it is not open, save the Gaussian input file and run Gaussian.

Gaussian's program path can be changed with:: menuselection: Tools –> Preferences –> Program Path.

Following file will be generated with execution. For example, the file/folder name when the input file is: file: water.gjf is shown together.

type	Description
log file water.log	Calculation log file.
bat file water.gjf.bat	It is a batch file for running Gaussian.
Working folder water_gau_tmp\	Working folder.

The job is run through Winmostar Job Manager.

6.8.4. Open Log File (log/out)

Open the log file with a text editor.

6.8.5. Animation

6.8.5.1. Optimization

Creates and displays animation of structural optimization calculation from information of log file.

For the animation display operation method, see Animation display area.

6.8.5.2. IRC/modred

Creates and displays animation of IRC calculation from information of log file.

For the animation display operation method, see Animation display area.

6.8.6. Analyses

6.8.6.1. Molecular orbitals, Charge

Retrieve and display molecular orbital and charge information from log 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.

6.8.6.2. UV-Vis Spectra

Displays UV-Vis spectra from log file information.

Refer to IR Spectrum Window for how to operate the subwindow.

6.8.6.3. See UV-Vis Spectrum window for subwindow operation.

Display NMR spectra from log file information.

See NMR Window for subwindow operation.

6.8.6.4. IR/Raman

Displays vibration spectra (IR or Raman spectra) from information in the log file.

Refer to IR Spectrum Window for how to operate the subwindow.

6.8.6.5. RESP Charges

Calculate the point charge based on the RESP method from the esp file.

The esp file to be read must have been output from a calculation performed by selecting RESP/ESP in Configure ‣ Easy Setup. Spin multiplicity is assumed to be 1. Internally, RESP charge is calculated using Antechamber.

To use this function, you need to use G09.C.01 or later version; if you use the version before G09.C.01, you need to change the IOP.

Warning

To use this function, CygwinWM setup is required.

6.8.7. FormChk

Launch Formchk in the G16W, G09W, and G03W utilities to create and display formatted .fch files from .chk files.

6.8.8. Import Fchk (Cubegen) File

Run Cubegen from the G16G, G09W, or G03W utility and create a Cube file by reading the .fch file. If Cubegen is not available, use Winmostar’s built-in OpenCubegen.

For how to operate the subwindow, please refer to Surface Setup window and the following.

Property

MO

Molecular orbital

Density

Electron density

ESP

ESP

Spin

Spin density (alpha - beta)

Alpha

alpha spin density

Beta

beta spin density

Current Density

Current Density

Shielding Density

Shielding Density

Type

Specify the option of the Density keyword. (HF, MP 2, CI, QCI)

Cube

Output the Cube file.

OpenCubegen supports fchk files up to approximately 2 GB. The upper size limit depends on the molecule size and basis functions. We plan to remove the fchk file size limitation in the future.

6.8.9. Import Cube File

Read and display the Cube format file.

For GAMESS pun file, convert it to Cube file.

For how to operate the subwindow, please refer to Surface Setup window and the following.

cube Manipulation

Perform operations on cube files specified in File 1 and File 2.

map

Map the data in the lower column to the data in the upper column. (Example mapping ESP to Density)

subtract

We will cover the difference between the data of the two cube files.

sub 2

We will cover the difference between the squares of the data of two cube files.

add

We will cover the sum of two cube files.

Cube

The calculation result of the cube file targeted by Map is output and displayed.

Cubegen

Start Cubegen, read the fch file and create a Cube file. For details, see Import Fchk (Cubegen) File.