6.8. menu
It is a menu about Gaussian.
In order to use Gaussian you need to install Gaussian separately.
6.8.1. Workflow Settings
Sets up and executes the Gaussian computation flow in project mode. Local jobs in project mode will use the binary specified in Gaussian in .
- Preset
Recalls and saves a preset of settings.
- # of Jobs
Specifies 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 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., when you open an SDF file).
After the scan calculation is finished, use to tabulate the calculation results.
- Import
Load 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. Note that CHelpG charges are read as ESP charges when the log file is read.
- Method
Specify the calculation method (Hamiltonian).
- Basis set
Specify the set of basis functions.
- Charge
Specify the value of the charge.
- Multiplicity
Specify Spin multiplicity.
- Solvent
Specify solvent type and solvent calculation method.
6.8.2. 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 .
- 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
Only IR intensity is calculated and Raman intensity is not obtained.
- 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
- td
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.
- Config ONIOM
Set up ONIOM calculation. You must have assigned each atom to a layer with beforehand.
- Hamiltonian
Set the Hamiltonian for each layer.
- Basis
Sets the basis function for each layer.
- 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.
- fchk
Create the Test.FChk file.
- counterpoise
Perform a counterpoise calculation. The fragment number set for each atom is assigned the residue number on Winmostar. Note that the Assign different residue numbers to each molecule. function can be used to assign different residue numbers to each molecule at once.
- 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.
6.8.3. Import Keywords
Only keywords (calculation conditions) are read from the existing Gaussian input file.
6.8.4. 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
water.logCalculation log file.
water.gjf.batIt is a batch file for running Gaussian.
water_gau_tmp\The job is run through Winmostar Job Manager.
6.8.5. Open Log File (log/out)
Open the log file with a text editor.
6.8.6. Animation
6.8.6.1. Optimization
Creates and displays animation of structural optimization calculation from information of log file.
For the animation display operation method, see Animation operation area.
6.8.6.2. IRC/modred
Creates and displays animation of IRC calculation from information of log file.
For the animation display operation method, see Animation operation area.
6.8.7. Analyses
6.8.7.1. 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 and so on.
See Energy Level Diagram window , Surface Setup / Cubgen window for subwindow operation.
6.8.7.2. UV-Vis Spectra
Displays UV-Vis spectra from log file information.
Refer to IR Spectrum Window for how to operate the subwindow.
6.8.7.3. See UV-Vis Spectrum window for subwindow operation.
Display NMR spectra from log file information.
See NMR Window for subwindow operation.
6.8.7.4. 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.
6.8.7.5. 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 . 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.
Assigning ONIOM layers
- Show Layer Flags
Displays the flags for the layers assigned to each atom.
- Unset Layers for All Atoms
Delete flags for all atom layers.
- Select Atoms in High/Middle/Low Layer
Group selection of atoms set to High/Middle/Low Layer, used to confirm atoms set to High/Middle/Low Layer.
- Set Selected Group to High/Middle/Low Layer
Set the atom of the selected group to High/Middle/Low Layer.
- Select All
Group selection of all atoms.
- Select None
Deselect group selection.
6.8.9. FormChk
Launch Formchk in the G16W, G09W, and G03W utilities to create and display formatted .fch files from .chk files.
6.8.10. 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 / Cubgen 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.
6.8.11. 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 / Cubgen 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.