NAMD

NAMD v2.12

This is the NAMD version 2.12 Scalable Molecular Dynamics package.

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

#!/bin/bash
#
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=40
#SBATCH --time=11:00:00
#SBATCH --job-name namdtest

# Note that the module will likely be taken out of experimental mode at some point.
module load namd/.experimental-2.12-ibverbs-smp

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

# EXECUTION COMMAND; -np = nodes*ppn
charmrun ++p 80 namd2 +idlepoll input.namd

The above script requests 2 nodes and runs namd on 80 processors.

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