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Gromacs

General Information

Short Description: Gromacs is molecular dynamics software that is primarily for biochemical molecules.

Category: Computational Chemistry

Installation Information

Versions:  3.3.1, 3.3.2, 4.0.4     Version Date:  2009

Technical support:  Please contact reserchservices@bc.edu

Terms of Use:  

License Information

Number of Licenses:  Licenses for use on the Linux Cluster.

Type of License:  GNU General Public License

Installed Sites: Linux Cluster.

Installed Platforms: Linux

Vendor/Developer: 

Vendor Website: www.gromacs.org

Usage Information

To use gromacs, first load the gromacs module by typing:

    module load gromacs

To submti jobs to the queues, create a script file.  In this example we will use the file named gromacs.pbs.  Then type"

    qsub  groamcs.pbs

The sample script file, gromacs.lsf, below requests 4 processors on one node, 4 GB of memory and 1 hour and 24 hours of time.

#!/bin/tcsh
#PBS -l pmem=4gb,nodes=1:ppn=4,walltime=24:00:00

module load torque mpich2 gromacs   
rm -rf \#*

mpiexec -np 4 -v -s md_81.tpr -o md_81.trr -cmd_81_out_gro -e ener_81 -g md81_log

You need replace md_81.tpr in gromacs.pbs to your own input file

Documentation

Documentation is available at www.gromacs.org.  There are also man pages available on the Cluster.