Gaussian Notes

1. CONTACTS

  • Tam V.T. Mai (Mr.), thanhtam010388@gmail.com
  • Ngoc N. Ho (Ms.), hnngoc.hcmiu@gmail.com

2. TUTORIALS

3. RUNNING GAUSSIAN

@ ICST

  • 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 C2H6.com
      • 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: (https://www.nchc.org.tw/en/inner.php?CONTENT_ID=675)
    • 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

4. INPUT CONSTRUCTION

To create a Gaussian input file, open a text editor on your PC, e.g. Notepad or Notepad++ (https://notepad-plus-plus.org/) 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.

5. TROUBLE SHOOTING

5. GAUSSIAN 09W TUTORIAL

Please click here

6. TROUBLE SHOOTING

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?

A4:

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

A5:

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.