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NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. Documentation and source code on the web page of “Theoretical and computational biophysics group

There are few possibilities to start NAMD simulation on the MOGON cluster.

<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>

This starts one threaded simulation direkt on the login host. Input configuration file describes simulation. Complete description of the input file format is available in the NAMD Documentation.

Using threaded start allows to achieve performance increasing:

bsub -R “affinity[core(<number of cores>)]” <PATH TO NAMD INSTALLATION>/namd2 +p<number of threads> <input configuration file>

where <number of threads> is normally equal to <number of cores>. For example

bsub -R “affinity[core(16)]” <PATH TO NAMD INSTALLATION>/namd2 +p 16 <input configuration file>

starts NAMD simulation with 16 threads using 16 cores of a node.

Mogon cluster contains different nodes with up to 64 cores.

On machines with more than 32 cores it may be necessary to add a communication thread and run on one fewer core than the machine has. For example on a 64-core machine this would be run as

bsub -R “affinity[core(64)]” <PATH TO NAMD INSTALLATION>/namd2 +p 63 +commthread <input configuration file>

  • namd.1403001170.txt.gz
  • Last modified: 2014/06/17 12:32
  • by noskov