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NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
To determine the available versions of NAMD installed use
$ vpkg_versions namd Available versions in package (* = default version): namd NAMD - Scalable Molecular Dynamics 2.8 Version 2.8 (Compiled with GCC) * 2.9 Version 2.9 (Compiled with Intel Compilers)
Batch job
Templates for Grid Engine queue submission scripts are available for serial or parallel batch NAMD jobs on Mills in /opt/templates/gridengine/namd. Copy and edit the template based on your job by following the usage described in the named-serial.qs or named-parallel.qs, respectively.
It is a good idea to periodically check if the template
/opt/templates/gridengine/namd has changed as we learn more about what works well on a particular cluster.