Updated 2023-03-31

Run NAMD on the Cluster


  • NAnoscale Molecular Dynamics is computer software for molecular dynamics simulation written using the Charm++ parallel programming model.
  • This guide will cover how to run NAMD on the Cluster.
  • For more information about NAMD, please visit the NAMD Tutorial Page.


  • NAMD uses a Protein Data Bank (pdb) file, a Protein Structure File (psf), a force field parameter file, and a configuration file to set up a molecular dynamics simulation.

Walkthrough: Run NAMD on the Cluster

  • The example covered in this walkthrough will have the user examine the ApoA1 tutorial.
  • apoa1 folder can be found here
  • SBATCH script can be found here

Part 1: The SBATCH Script

#SBATCH -JnamdTest
#SBATCH -A [Account]
#SBATCH -N1 --ntasks-per-node=8
#SBATCH --mem-per-cpu=2G
#SBATCH -t15
#SBATCH -qinferno
#SBATCH -onamdOutput.out

module load namd
namd2 apoa1/apoa1.namd
  • The #SBATCH directives are standard, requesting just 3 minutes of walltime and 1 node with 8 cores. More on #SBATCH directives can be found in the Using Slurm on Phoenix Guide
  • $SLURM_SUBMIT_DIR is a variable that represents the directory you submit the SBATCH script from. Make sure the files you want to use are in the same directory you put the SBATCH script.
  • Output Files will also show up in this dir as well
  • module load namd/2.14_ibverbs loads the 2.14 version of NAMD. To see what versions of a software are available, run module avail [Software], and load the one you want. The other modules are dependencies that must be loaded before NAMD is loaded.
  • namd2 apoa1/apoa1.namd will have Namd carry out the operation.

Part 2: Submit Job and Check Status

  • Make sure you're in the dir that contains the SBATCH Script as well as the apoa1 folder
  • Submit as normal, with sbatch < script name>. In this case sbatch namd.sbatch
  • Check job status with squeue --job <jobID>, replacing with the jobid returned after running sbatch
  • You can delete the job with scancel <jobID> , replacing with the jobid returned after running sbatch

Part 3: Collecting Results

  • In the directory where you submitted the SBATCH script, you should see a Report-<jobID>.out file which contains the results of the job.
  • Report-<jobID>.out should look like this
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran NAMD on the cluster.