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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 (it's not permitted). Input configuration file describes simulation. Complete description of the input file format is available in the NAMD Documentation.

  • namd.1402998834.txt.gz
  • Last modified: 2014/06/17 11:53
  • by noskov