Contents


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Introduction

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Version and availability

Version 4.0.7 is available on all Linux clusters.

Usage

Before running a GROMACS job, you need to add '+gromacs-4.0.7-intel-11.1-mvapich-1.1' to your .soft file and resoft ( For TeraGrid users, '+mvapich-1.1-intel-11.1' is also required and needs to appear before any other keywords in your .soft file). For more information on the .soft file and the resoft command, please refer to Managing the Environment with SoftEnv.

To run GROMACS through PBS, you need a script like the one below. In this example, GROMACS runs with 8 processors.

 #!/bin/bash
 #PBS -A your_allocation
 #PBS -q checkpt
 #PBS -l nodes=1:ppn=8
 #PBS -l walltime=12:00:00
 #PBS -V
 #PBS -j oe
 #PBS -N gromacs_test
 
 # mdrun_d is the MPI version of mdrun.  
 export EXEC=mdrun_d
 export WORKDIR=$PBS_O_WORKDIR
 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
   
 cd $WORKDIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -s fws_em.tpr \
        -o fws_em.trr -c fws_b4pr.pdb -e em.edr -g em.log

Then submit it to run (assuming that the script above is named rungromacs.pbs)

qsub rungromacs.pbs

References

A User Manual is available on line.


Users may direct questions to sys-help@loni.org.

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