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| software:gromacs:gromacs [2017-10-23 17:01] – created sraskar | software:gromacs:gromacs [2023-03-29 14:04] (current) – [Details by cluster] anita |
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| ====== GROMACS ====== | ====== GROMACS ====== |
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| [[http://www.gromacs.org/About_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. | [[http://www.gromacs.org|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. |
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| To determine the available versions of GROMACS installed use | To determine the available versions of GROMACS installed use |
| <code> | <code> |
| $ vpkg_versions gromacs | $ vpkg_versions gromacs |
| Available versions in package (* = default version): | |
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| [/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 | |
| </code> | </code> |
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| **Details by cluster** | =====Details by cluster===== |
| | * [[software:gromacs:caviness | Caviness]] |
| * [[software:gromacs:Mills]] | * [[software:gromacs:darwin | DARWIN]] |
| * [[software:gromacs:Farber]] | * [[software:gromacs:farber | Farber]] |
| ===== Batch job ===== | * [[software:gromacs:mills| Mills]] |
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| 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''. | |
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| <note tip>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.</note> | |