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GROMACS
GROMACS (GROningen MAchine for Chemical Simulations) is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
To determine the available versions of GROMACS installed use
$ vpkg_versions gromacs Available versions in package (* = default version): [/opt/shared/valet/etc/gromacs.vpkg] gromacs Gromacs: Molecular Dynamics * 4.5.5-open64 Version 4.5.5: double-precision with OpenMPI support, FFTW3 4.5.5-intel64 Version 4.5.5: single-precision with OpenMPI support, Intel MKL FFT 4.5.5-pgi12 Version 4.5.5: double-precision with OpenMPI support, FFTW3
Details by cluster
Batch job
Templates for Grid Engine queue submission scripts are available for batch GROMACS jobs in /opt/templates/gridengine/gromacs. Copy and edit the template based on your job by following the usage described in gromacs.qs.
It is a good idea to periodically check in
/opt/templates/gridengine/gromacs on a specific cluster for changes in existing templates, or the addition of new templates, designed to provide the best performance for a particular version of GROMACS on that cluster.