NAMD

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is file-compatible with AMBER, CHARMM and X-PLOR.

Please read the license agreement.

 Sample scripts for NAMD use are available in directory /opt/packages/examples/namd on Bridges.

Documentation

  • NAMD web site
  • Example scripts:  There are optimized example scripts for NAMD on Bridges in directory /opt/examples/namd.

Usage

To see what versions of NAMD are available type

module avail namd

To see what other modules are needed, what commands are available and how to get additional help type

module help namd

To use NAMD, include a command like this in your batch script to load the NAMD module:

module load namd

Be sure you also load any other modules needed, as listed by the module help namd command.

 

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