NAMD

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NAMD v2.9

This is the NAMD version 2.9 Scalable Molecular Dynamics package.

It was built directly on top of ibverbs, so it will only run on InfiniBand nodes. Here is a sample run script:


#!/bin/bash
# MOAB/Torque submission script for SciNet GPC (InfiniBand)
#
#PBS -l nodes=2:ppn=8,walltime=1:00:00,os=centos6computeA
#PBS -N namdtest

module purge
module load gcc openmpi/1.4.4-gcc-v4.6.1 namd/2.9-ibverbs-smp

# DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from
cd $PBS_O_WORKDIR

# EXECUTION COMMAND; -np = nodes*ppn
$SCINET_NAMD_HOME/charmrun ++verbose ++p 16 ++mpiexec ++remote-shell $SCINET_NAMD_HOME/namdmpiexec $SCINET_NAMD_HOME/namd2 water-salt.conf >& o/WATER_SALT.log

The above script requests 2 nodes with ib interconnect, and runs namd on 16 processors.

Full documentation for NAMD is available on their website: http://www.ks.uiuc.edu/Research/namd/