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| software:namd:farber [2018-11-15 19:43] – created anita | software:namd:farber [2021-04-27 16:21] (current) – external edit 127.0.0.1 |
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| ====== NAMD on Farber ====== | ====== NAMD on Farber ====== |
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| [[http://www.ks.uiuc.edu/Research/namd/|NAMD]] (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | |
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| To determine the available versions of NAMD installed use | |
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| <code> | |
| $ vpkg_versions namd | |
| </code> | |
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| ===== Batch job ===== | ===== Batch job ===== |
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| Templates for Grid Engine queue submission scripts are available for serial or parallel batch NAMD jobs on ''Mills'' & ''Farber'' 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. | Templates for GridEngine queue submission scripts are available for serial or parallel batch NAMD jobs on ''Farber'' in ''/opt/shared/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. |
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| <note tip>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.</note> | <note tip>It is always a good idea to periodically check if the templates in ''/opt/shared/templates/gridengine/namd'' have changed especially as we learn more about what works best on a particular cluster.</note> |