Computational Chemistry User Guide

 

Running Gromacs on Mercury

 

 

Please consult the on-line user guide for a more detailed description about Gromacs. 

 

 

As an example, we will run the dppc benchmarks calculation with 32 processors. 

 

1.  Copy the files from the sample directory into your working directory:

 

tg-login:% cp /usr/projects/chemistry/gromacs/sample/* .

 

2.  Run grompp

 

tg-login:% /usr/projects/chemistry/gromacs/gromacs-3.2.1/ia64-unknown-linux-gnu/bin/grompp –np 32

 

3.  Submit gromas job:

 

tg-login:% qsub gromacsjob