GROMACS

GROMACS is a versatile package of molecular dynamics simulation programs. It is primarily designed for biochemical molecules, but it has also been used on non-biological systems.  GROMACS generally scales well on OSC platforms. Versions after 4.6 include GPU acceleration.

Availability & Restrictions

GROMACS is available to all OSC users without restriction.

The following versions of GROMACS are available on OSC systems:

Version Glenn Oakley
3.3.1 X  
3.3.3 X  
4.0.3 X  
4.5.4 X  
4.5.5 X X
4.6.3   X

Usage

Set-up

Initalizing GROMACS on both Glenn and Oakley is done by loading a gromacs module:

module load gromacs

To see other available versions, run the following command:

module avail

Using GROMACS

To execute a serial GROMACS program interactively, simply run it on the command line, e.g.:

pdb2gmx

Parallel GROMACS programs should be run in a batch environment with mpiexec, e.g.:

mpiexec mdrun_mpi_d

Note that '_mpi' indicates a parallel executable and '_d' indicates a program built with double precision.

Batch Usage

Sample batch scripts and GROMACS input files are available here:

/nfs/10/srb/workshops/compchem/gromacs/

This simple batch script for Oakley demonstrates some important points:

# GROMACS Tutorial for Solvation Study of Spider Toxin Peptide
# see fwspider_tutor.pdf
#PBS -N fwsinvacuo.oakley
#PBS -l nodes=2:ppn=12
module load gromacs
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cd $PBS_O_WORKDIR
pbsdcp -p 1OMB.pdb em.mdp $TMPDIR
# Use TMPDIR for best performance.
cd $TMPDIR
pdb2gmx -ignh -ff gromos43a1 -f 1OMB.pdb -o fws.gro -p fws.top -water none
editconf -f fws.gro -d 0.7
editconf -f out.gro -o fws_ctr.gro -center 2.0715 1.6745 1.914
grompp -f em.mdp -c fws_ctr.gro -p fws.top -o fws_em.tpr
mpiexec mdrun_mpi -s fws_em.tpr -o fws_em.trr -c fws_ctr.gro -g em.log -e em.edr
cat em.log
cp -p * $PBS_O_WORKDIR/

Further Reading

 

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