Using NAMD at the HPC 

• NAMD is compiled using mvapich version 1 (takes advantage of the infiniband fabric)
• Must the following submission file can be used as an example.
• To increase the number of processes, change the nodes and ppn MOAB parameters accordingly and also the arguments to "+p" and "-np"  to correspond to the same number processors.  

Example MOAB script for namd2. 

#!/bin/bash

#MOAB -lnodes=1:ppn=2
#MOAB -j oe -N namd

source /usr/local/profile.d/mpichv1-gnu.sh

/panfs/storage.local/system/export/NAMD-2.6/charmrun \
+p2 -np 2 -machinefile $PBS_NODEFILE \
/panfs/storage.local/system/export/NAMD-2.6/namd2 alanin

Jeff McDonald -- Sept 17, 2006