You can run the small 3-21G calculations on a laptop or desktop computer easily However, larger calculations will take longer, and you should run them on the high performance computer. Submission is via a web-portal. First create the job as normal and save the input file, however do NOT submit the job to run.
important put your name or initials in the filename otherwise it is possible the servers will have 28 files with the same name and your job will not work correctly. Give your files descriptive names because after running a few jobs you will forget which one is which. The server will assign your file a unique name but this is not very descriptive, rename the file when you get it back from the server.
important Do not use special characters or spaces in file names. In unix spaces and special characters have a special meaning and you could run into problems, I use "underscore" instead of spaces.
create a project for your jobs by clicking on the projects tab and creating a new project (only do this once!):
then create a new job, by clicking on the "New Job" tab, leave "Chemistry Lab 1" button as is and click continue:
next under "select application type" click on the "Amber PMEMD" button and select Gaussian 1px. Then press continue. Do not use the 4px or 8px queues, they are for much larger jobs than yours! If you are tempted by the larger queues don't be, the amount of time to set up the parallel run will excede the runtime on your job, and it will take longer to run!
browse your drive to find your saved input file select it and then add a job description (this is important because if you submit a number of jobs you want to know what each one is!). Then click submit.
Now click on the "Job List" tab to see if your job is still in the queue or if it has gone in and run and is now finished. My job below has finished:
When your job has finished:
check that the file type you want to download is selected, usually this is either the .log OR the .chk file, here I have selected the .log file
click on download to save the file back to your computer for inspection and analysis
depending on your browser download options the file may be in a "Downloads" directory, so you will need to move it into your "year3_lab" directory with your other files for this lab.
the file will have a new name assigned by the scan server, change the name back to the one you gave it originally. For example my file came back called log_100112.log and I renamed it back to AsBr3_pp_opt1.log. Renaming is important because once you have a large number of files you want to be able to know which is which.
Then you can procede to open the file in gaussview and continue with your checks and analysis.
