Introduction

NAMD is a powerful molecular dynamics program design to simulate large biomolecular systems in a manner which is scalable across large numbers of processors.

Using NAMD on RCC Resources

NAMD is available on the HPC and Spear using the Intel Compilers and MVAPICHv2. It automatically receives the number of processors you wish to run on when you submit NAMD jobs via the Slurm Scheduler. This version also interprets TCL commands in configuration files.

The binary executable for namd is available at the following filesystem location:

/opt/hpc/intel/mvapich2/bin/namd2

To submit NAMD jobs to Slurm, refer to the following example submission script:

#!/bin/bash

#SBATCH -N 8
#SBATCH --job-name="namd"
#MOAB -t 10:00:00
cat $SLURM_JOB_NODELIST
module load intel-mvapich2
export NAMD=/opt/hpc/intel/mvapich2/bin
cd $SLURM_SUBMIT_DIR
pwd
srun $NAMD/namd2 CONFIG.namd +isomalloc_sync > namd.`date +%Y%m%d.%H%M%S`.log