Gaussian 09 is the workhorse of computational chemistry and can be used to optimise molecular geometry in gas and solution phase. Also can be used to find transition states and calculate physical properties and observables, such as charge distribution, energy, volume, and dipole.

Gaussian has very good documentation on which commands to use:

e.g. https://gaussian.com/opt/

List of important keywords:

• [method/basis set] e.g. b3lyp/6-31+G(d) (the type of electronic method with which to run the calculation) 

• b3lyp/gen (use different basis sets for different elements, defined later in the input)

• b3lyp/genecp or pseudo=read (use electron core potential for heavy atoms such as metals, defined later in the input)

• opt (optimise the geometry of the molecule provided)

• freq (run a frequency calculation on the molecule)

• SCRF=(solvent=acetone) (the implicit solvent in which to run the calculation)

https://docs.computecanada.ca/wiki/Gaussian_error_messages

Error: Solutions

• Convergence criteria not met: Add SCF=XQC in .com file; Change basis set; Get new starting structure

• link 9999 (geometry not optimised): Restart from last structure; Use less intense method (e.g. PM6); Get new starting structure

• FormBX error; Linear angle in bend; Linear angle in Tor: Add opt=cartesian to .com file; Restart from checkpoint with:Opt=ReadFC Geom=(CheckPoint, NewDefinition) Guess=Read

• Memory error: Make sure .sh and .com file are set up as above

• Atom out of range for basis set: Use different basis set; Use different basis set for just that atom

Gaussian requires 2 files to run. Firstly a .sh file. This provides the details to the supercomputer to run your job in Gaussian. Secondly a .com file. This file contains an initial starting structure and a set of commands for Gaussian to run on the molecule.

Sample .sh file

Sample .com file

To use separate basis sets for different atoms set up the .com file as shown below.

Sample .com with split basis sets

Once the files have set up, use:

To submit the job:

qsub file_name.sh

To submit multiple jobs (this would submit every .sh file in the folder):

for f in *.sh; do qsub "$f"; done

Or for submitting jobs in subfolders:

find . -type f -name "*.sh" -exec dos2unix {​​}​​ \;
find . -type f -name "*.sh" -exec qsub {​​}​​ \;

To check on the status of the job:

qstat

To count the number of queued job for an user:

qstat -u username | wc -l

To terminate the job:

qdel job_id

Using the OptX functional (eg. OV5LYP) with custom scaling values is bugged in Gaussian 09 Rev D.01 and an older software version is required.

When using the LANL2DZ basis set always use ECP, otherwise the structure will collapse

G09 uses the fine grid as default, G16 uses the ultrafine grid.

Custom D3 dispersion settings:

When using D3 parameters not already included in G09, the values have to be specified in the .sh file using:

export GAUSS_DFTD3_<param>=value * 1,000,000

for example for TPSSh S8 = 2.2382:

export GAUSS_DFTD3_S8=2238200, a full example can be seen here.

Electronic States in frequency outputs:

Singlet = 1-A

Diradical triplet = 3-SGG

Triplet = 3-A

Newzmat is a tool installed along Gaussian to manipulate Gaussian files

https://gaussian.com/newzmat/

You can get the last structure in a .chk file thus:

module add gaussian
newzmat -ichk -oxyz FILE.chk FILE.xyz

You can get the nth structure in a .chk file thus:

module add gaussian
newzmat -ichk -oxyz -ngeom n FILE.chk FILE.xyz