Gaussian Notes


  • Tam V.T. Mai (Mr.),
  • Ngoc N. Ho (Ms.),




  • Job submission
    • Setup the environment:
      • Add the Gaussian path to bash shell in your home directory: $HOME/.bashrc
      • Type "source $HOME/.bashrc" to take in into effect
  • Useful PBS Commands: type "man <PBS_command>" for detailed instruction
    • "qsub": submits PBS job
    • "qstat": shows the status of PBS jobs
      • "qstat -a": list all jobs
      • "qstat -u hklam": list jobs of user hklam
    • "qdel": deletes PBS job
    • "pbsnodes": shows the detail of nodes
    • "checkjob <jobID>": shows the current status of the job
      • "checkjob 11234": check the job with ID 11234

@ IU

  • Job submission:
    • Syntax: sub_g09 <input-filename> <core-number> <hours>
      • Filename: works for .com extension only, namely
      • Ex: sub_g09 C2H6 4 12

@ Utah

  • Job submission:
  • Gaussian input:

@ Clemson

  • Job submission:
  • Gaussian input:

@ Taiwan (Kuang's cluster)

  • Job submission:
  • Gaussian input:

@ MC Lin's cluster

  • Job submission: g09sub {gaussianj-job-name-without-extension-of-com}
  • Useful Commands: (
    • 1. "llq": to query all jobs
    • 2. "llq -u <USER>": to query your own jobs
    • 3. "llstatus": to check the status of the computing nodes
    • 4. "llclass": to show the details of jobs class
    • 5. "llcancel <JobID>": to cancel your job via JobID


To create a Gaussian input file, open a text editor on your PC, e.g. Notepad or Notepad++ ( and fill in the following information. Input sections marked with an asterisk are required in every input file.

Ref: "Exploring Chemistry With Electronic Structure Methods", 2nd Edition by James B. Foresman (Author), AEleen Frisch (Author)

Common route sections in the input files: This section specifies the theoretical procedure, basis set, and desired types of calculation. The ordering of keywords is not important.



Please click here


Q1: What if I get more than one imaginary frequencies for a transition state?

A1: Eliminate the low frequencies so that there is only one imaginary frequency corresponding to the reaction coordinate (normally the biggest magnitude imaginary frequency)

  • Step 1: First, try to visualize the vibration corresponding to the identified small imaginary frequency. Then manually change the coordinates in the direction of this vibration (should be a very small change)
  • Step 2: Re-optimize using the option: opt=(calcfc, noeigentest, tight, ts) scf=qc
  • Step 3: If it still doesn't work try to freeze the part of the molecule(s) that are not moving in this vibration connected to the small imaginary frequency and do Step 2 (but then re-optimize with all coordinated unfrozen, even if the frozen one gives you only one imaginary freq).

Q2: How to plot iso-surfaces for a molecule?

A2: The simplest way is using Gaussview&Gaussian for Windows. Please follow the following steps:

  • Step 1: open the output file by Gaussview and click on "MOs..." option in the "View" dropbox
  • Step 2: go to "New MOs" tab, choose the MOs that you want to plot and click on "Generate" button to generate the .chk file
  • Step 3: go to "Visualize" tab and choose the MO that you want to plot and click "Update" button and that's it!

Q3: What is basis set superposition error (BSSE)? How to take it into account?

A3: Please click here for the answer

Q4: How to do the scan?


Q5: What if I get a transition state having lower energy than the stable species?


Q6: Convergence cannot be achieved?

A6: SCF=Tight is the default for G09. You should retry your computation after including SCF=XQC in the Route Section.