NAMD

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NAMD - Scaleable Molecular Dynamics[1] is available on the HPC system.

To access NAMD, either load the NAMD module: module load namd/2.10

Or set your path to access it in /opt/NAMD by adding the following to your .bashrc or .bash_profile: PATH=$PATH:/opt/NAMD/ export PATH

Example Job Script

#!/bin/sh
#PBS -l nodes=1:ppn=16
#PBS -N NAMD-test
#PBS -d /home/mtech/username/working_dir
#PBS -m e
#PBS -M username@institution.edu
#PBS -l walltime=01:00:00
module load namd/2.9
charmrun namd2 +p16 xxxxx.conf > yyyyy.txt

Note:

  • charmrun must be the first statement in order to load CHARM++ to the run
  • namd2 is the executable for NAMD
  • +p<#processes> => number of processes that will run on the node = same as the ppn value on top
  • xxxxx.conf => configuration file
  • yyyyy.txt => write output to file since NAMD writes to standard out