This is a guide for running a calculations with Gaussian 09. For an intro to the file structure of the inputs and outputs a good book is by Foresman and Frisch. Normal Use Setting up the pbs file for the first use Before the first time you try to use Gaussian 09 you need to be given access to use it, ask the system administrator for this. The following entries need to be changed before running a calculation • Change the working directory to the folder where you will have the input files located ##Enter your working directory here: #PBS -d /home4/ryelle/test/g09test • Change the file extensions to reflect the ones that you use, such as.gjf instead of.inp. Make sure the extension to the output file has the extension that you prefer, such as changing.out to.log. Sharam Party All The Time Acapella Download on this page. Inp /tmp/$USER g09 $CWD/$JOB.

Out Running a calculation This is assuming that you have a working pbs file directed to your folders. See above for doing this. • Create an input structure. This can be done easiest with Gaussview 5.

There is a Chemistry department license for the Windows version this. Alternatively there are free programs that are a bit less user friendly such as Avogadro. The is available online which is a helpful reference for input building. There is also a test job located in the INFO folder where the Gaussian PBS file is. Transfer the input file to ACISS. On Windows, WinSCP is great program for this.

• Update the variables in the pbs file. Name in queue #PBS -N g09_test queue to submit job to #PBS -q generic number of processors to use #PBS -l nodes=1:ppn= 12 set the filename here omitting the extension (this should be set already, see below) export JOB= g09_sample • Logon to ACISS and start the calculation by going to directory that has the pbs file in it and type: qsub g09.pbs to start the calculation. PuTTY is a great program for doing this on Windows. Guide to Plotting Molecular Orbitals So you have a finished calculation and now you want to see pictures of the molecular orbitals, electrostatic potential maps, and everything else there is. This is a quick walkthrough of how to get the data to plot them from the Gaussian 09 output. • Login to ACISS with PuTTY or a similar program • Request an interactive node by typing ‘qsub -I’ • Load the Gaussian module by typing ‘module load gaussian’ • Go to the folder where your output checkpoint file is (whatever it is named), chkname.chk. • Convert the checkpoint file to a formatted checkpoint file by typing ‘formchk chkname.chk’ There should now be a file chkname.fchk —There are now several ways to look at the MOs from the.fchk file— • Avogadro is the fastest and easiest way to see the MO plots, just open the.fchk file with this.