Gaussian Notes

1. CONTACTS

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

2. TUTORIALS

• Essential books (for beginners):
  • "Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian", 2nd Edition by James B. Foresman (Author), AEleen Frisch (Author)
• CASSCF, http://www.ch.ic.ac.uk/robb/casscf_benzene_handout.php

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:

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.