Currently, NAMD 2.7 is installed using the intel compilers with mvapich2 (pgi and gnu versions will be installed in the future).

Using NAMD at the HPC

• NAMD is compiled using mvapich2 which
  automatically receives the number of processors you requested
  and which nodes to run on.
• Use the following submission file as a template.
• This version interprets tcl commands in the configuration files.
• The binaries are installed on:
  /panfs/storage.local/opt/NAMD/NAMD_2.7

Example MOAB script for namd2.

#!/bin/bash

#MOAB -l nodes=8
#MOAB -j oe -N namd
#MOAB -l walltime=10:00:00

cat $PBS_NODEFILE

source /usr/local/profile.d/iccvars.sh
source /usr/local/profile.d/mpichv2-intel.sh

export NAMD=/panfs/storage.local/opt/NAMD/intel/bin

cd $PBS_O_WORKDIR
pwd

mpirun $NAMD/namd2 CONFIG.namd +isomalloc_sync > namd.`date +%Y%m%d.%H%M%S`.log