GROMACS Runtime Environment home page

Taken from http://www.gromacs.org: 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 information

Only this development version currently available.

Interface definition

The runtime environment takes care that Gromacs binaries are found in the default PATH. Most importantly, mdrun can be invoked with no extra arguments.

Examples

The job description file gromacs.xrsl

&
(executable=run_gromacs.sh)
(jobname=gromacs_serial)
(stdout=std.out)
(stderr=std.err)
(gmlog=gridlog)
(cputime=60)
(memory=1000)
(disk=4)
(&
  (runtimeenvironment>=APPS/CHEM/GROMACS-3.3.3)
)
(inputfiles=
  ("topol.tpr" "topol.tpr.serial")
)

The job script is very simple

#!/bin/sh
echo "Hello Gromacs!"

mdrun
exitcode=$?

echo "Bye Gromacs!"
exit $exitcode

System administrator guide for installing the RE

Gromacs binaries

See separate installation guide.

Runtime environment script

Here is a sample runtime environment script. Gromacs makes it extremely easy by providing an environment bootstrap script GMXRC.

#!/bin/bash
#
# Nordugrid ARC runtime environment script for Gromacs serial runs.
#

# shared directory for application installation 
application_base_path='/grid/nordugrid-arc/appl/'
# version
gromacs_version='3.3.3'

case "$1" in
0 )
    # nothing to do on the frontend
;;

1 )
    # source the Gromacs environment on the node
    source $application_base_path/gromacs/$gromacs_version/bin/GMXRC        
;;

2 )
    # nothing to clean up
;;

* )
    # Now, calling argument is wrong or missing.
    # If call was made from NorduGrid ARC, it is considered
    # an error. If this script is to be used also to initialize
    # MPI environment for local jobs in cluster, raising error here
    # could be improper.
    return 1
;;
esac

Contact information

Contact olli.tourunen@csc.fi if you have any grid use specific questions. Contact your local Gromacs guru in MD related questions.