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NAMD

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General Description

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit Ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Restricted Software: You must agree to the NAMD User License Conditions before you can gain access to the NAMD software.

Basic Usage

To run a NAMD job in parallel, please use the following template as an example:

#!/bin/csh

#$ -pe mpi-12 24
#$ -m ae
#$ -M netid@nd.edu
#$ -q long

module load namd            # load NAMD module

mpirun -np $NSLOTS namd2 ./config-file​

User License Restrictions

Before you can be granted access to the NAMD software, please review the following user license conditions. Once you have read and agreed to the conditions please email CRC Support with your confirmation, after which you will be added to the NAMD software access group.

Media:NAMD_User_License_Conditions.pdf

Further Information

  • See the official website: NAMD