How To: Set up Gaussian Jobs

This page discusses setting up Gaussian calculations with GaussView. It deals only with the mechanics of doing so. Consult the Gaussian User’s Reference for detailed information about all Gaussian keywords and options.

Related Information:

The Gaussian Calculation Setup Window

Once the desired molecule is completed, you can use the Calculate=>Gaussian Calculation Setup menu path to open the Gaussian Calculation Setup dialog. It is illustrated below:


The Gaussian Calculation Setup Dialog

This dialog allows you to set up virtually all types of Gaussian calculations and to submit them from GaussView. The route section that GaussView is generating appears at the top of the dialog, and it is constantly updated as you make selections in the dialog’s various panels.

The dialog contains the following panels:

The Additional Keywords field below the panel area is used to enter any desired Gaussian keyword and/or option. Note that you must include the keyword for every option in this field even if it already appears in the route section as a result of panel item selection.

Below the panel area is the Calculation Scheme area. The controls have the following uses:

The buttons at the bottom of the dialog have the following effects:

 

Special Considerations for Various Gaussian Job Types

This section summarizes information about setting up various Gaussian job types for which some special steps are required.

Transition Structure Optimizations: Opt=QST2 and Opt=QST3

Gaussian STQN-based transition structure optimizations require two or three structures as input. To set up these jobs, you must create a molecule group containing the required number of structures. Once you have done so, the TS (QST2) and TS (QST3) options will be enabled in the Optimize to a field for the Optimization job type in the Job panel of the Gaussian Calculation Setup dialog.

If you plan on running an Opt=QST3 job, then the transition structure initial guess is assumed to be molecule 3 unless you specify a different structure on the Job Type panel.
g_qst3_ts.tif

Verifying and Specifying Atom Equivalences: In most cases, GaussView will automatically identify the corresponding atoms in the multiple structures for these transition state optimizations. However, you can verify this using the Connection Editor, accessed via the Connection Editor button on the toolbar or the Tools=>Connection Editor menu item. Connection Editor details here.

Warning: The atoms in the various molecules used for these two job types must be identical. If GaussView detects any ordering discrepancy, the option will be disabled on the Optimize to a dropdown.


Calculations on Polymers, Surfaces, and Crystals

You can set up jobs for Gaussian’s Periodic Boundary Conditions facility using the Crystal Editor (reached via the Crystal Editor button or the Tools=>PBC menu path). Once you have defined a unit cell, GaussView automatically sets up PBC jobs for this structure by including the translation vectors within the molecule specification. This is indicated by the enabling of the PBC panel in the Gaussian Calculation Setup dialog and the checked Use PBC item. Note that, for normal cases, you do not need to access this panel at all and can proceed directly to setting up Gaussian input in the normal manner.


Multi-Layer ONIOM Calculations

GaussView contains several features for setting up ONIOM calculations.


Specifying CASSCF Active Spaces Using Guess=Permute

GaussView can make it easy to specify CASSCF active space. The MOs dialog allows you to generate, view, select, and reorder the starting orbitals. It is reached with the Tools=>MOs menu path and via the MO Editor button on the toolbar. More details here.


Modifying Redundant Internal Coordinates (Geom=ModRedundant)

You can specify additions and other modifications to redundant internal coordinates for geometry optimizations and other jobs by using the Redundant Coordinate Editor, reached via the Redundant Coordinate Editor button on the toolbar or the Edit=>Redundant Coordinates menu path.


Freezing Atoms During Geometry Optimizations

The Atom Group Editor can be used to specify atoms whose positions are to be held fixed during a geometry optimization via its Freeze Atoms group class. This class is defined with four groups by default, corresponding to unfrozen atoms, frozen atoms, and the first two ONIOM frozen rigid blocks (freeze settings of -2 and -3; see the discussion of the Geom keyword in the Gaussian User’s Reference for full details on specifying frozen atoms and rigid blocks for ONIOM calculations). In order to hold specific atoms fixed during a geometry optimizations, add them to the Freeze (Yes) group.


Selecting Normal Modes for Frequency Calculations (Freq=SelectNormalModes)

g_normalmodes.tif
You can use the Atom Group Editor to select atoms for which normal mode analysis is conducted (see the Gaussian User’s Reference for details). Placing the desired atoms into the Select Normal Modes (Yes) group will cause them to be entered into the Atoms field corresponding to Select Normal Modes in the Gaussian Calculation Setup’s Job Type panel for Frequency jobs. You can modify this list manually as needed, but doing so will have no effect on the definition of the groups in the Atom Group Editor’s Select Normal Modes group class.


Setting up Scan Calculations

Different procedures are required for rigid scans and relaxed scans.

Relaxed Scans

When setting up a relaxed scan calculation, you first must specify coordinates to be scanned in the Redundent Coordinate Editor.

For this example, we will be scanning the bond between two benezene rings as they rotate about each other. The initial bond is 90 degrees, and we wish to take 9 steps of 10 degrees each. First, click the Add button, and then select Dihedral from the dropdown menu. Change the second dropdown to Scan Coordinate.Now click on the dihedral you wish to scan in the View window. The Coordinate: fields in the Redundent Coordinate Editor dialog will fill in with the atoms you have selected. Two new input fields will appear allowing you to specify the number of steps and each step size in the scan. For our example, we fill in 9 steps of 10 degrees.

scan_step1.tif
Adding a Scan Variable with the Redundant Coordinate Editor

When you open the Gaussian Calculation Setup’s Job Type panel, Scan, Relaxed (Redundant Coord) is already filled in, meaning the calculation will run with the settings you specified in the Redundant Coordinate Editor. In the Gaussian Calculation Setup’s Preview panel, which is shown below, you can see the input created by the Redundant Coordinate Editor at the end of the input.

scan_step4.tif
Previewing the Relaxed PES Scan Calculation Input

Rigid Scans

To set up a rigid scan calculation, we use the Atom List Editor to identify the structural parameters to be scanned. For this example, we open the Atom List Editor and then click on the Z and 0 buttons to display the Z-Matrix and Optimization Flags columns. We want to scan the C2-C3-C12-C13 dihedral angle. We locate this in row 13 of the table. In the Opt 3 column for this row, we change Yes to Rxn/Scan.

scan_step2.tif
Adding a Scan Variable for a Rigid Scan with the Atom List Editor

We close the Atom List Editor and then open the Gaussian Calculation Setup’s Job Type panel and select Scan, and Rigid for the scan type. The Scan Coordinate 1 subpanel shows the scan coordinate. Here you can specify the number of steps, the step size and/or end value. Changing any value causes the other boxes to automatically update. For example, by changing the number of steps and the desired end value, GaussView will automatically calculate the step size. In our example, we specified 9 steps of 10 degrees. The Preview panel dialog on the right shows the scan input included within the molecule specification.

scan_step3.tif
Input Setup for a Rigid Scan


Calculating NMR Spin-Spin Coupling: NMR=(SpinSpin,ReadAtoms)

When you select an NMR calculation in the Gaussian Calculation Setup’s Job Type panel, the field to the left appears. The atom list in the parentheses corresponds to the members of the NMR Spin-Spin (Yes) group, as defined in the Atom Group Editor (by default, all atoms are placed into this group, and the list of atoms reads all atoms). A specific group of atoms appears in this item when the NMR Spin-Spin (No) group contains at least one atom.


Specifying Fragment-Specific Charges and Spin Multiplicities

You can specify individual charge and spin multiplicity values for each fragment defined via the Atom Group Editor. This facility is useful for setting up fragment guess jobs (Guess=Fragment) for modeling antiferromagnetic coupling, counterpoise calculations (Counterpoise) for computing counterpoise corrections and basis set superposition errors, and the like. The image below illustrates setting up a system for modeling antiferromagnetic coupling effects.

eg_antiferro.tif
Specifying Per-Fragment Charge and Spin

Antiferromagnetic coupling is an effect that is important for molecules with high spin multiplicity. This Fe2Cl6 compound is a simple example. Here, we have defined three fragments. Each iron atom is in its own fragment, and the six chlorine atoms are in a third fragment. The two iron fragments are each assigned a charge of +3, and both are defined as sextets with opposite spin (i.e., spin multiplicities of 6 and -6). The fragment containing the chlorine atoms is defined as a singlet with a -6 charge. These values will be placed into the route section of the Gaussian job set up in GaussView.

The Gaussian Calculation Setup’s General panel contains features relevant to these two calculation types: Write Gaussian Fragment Data (for both types) and Use Counterpoise (for Counterpoise calculations). In addition, the Guess panel has two items useful for the first job step of a fragment guess job: Only do Guess (no SCF) and Use fragments (atom groups) for generating guess, corresponding to Guess=Only and Guess=Fragment (respectively). Typically, such a job would be followed by a second job to compute the energy including the antiferromagnetic coupling: Guess=Read Geom=AllCheck Stable=Opt.