Namd

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:

<source lang="bash">

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

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

1. DIRECTORY TO RUN - $PBS_O_WORKDIR is directory job was submitted from

cd $PBS_O_WORKDIR

1. 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 </source>

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/