Namd

Introduction

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. For more information, please check: NGC: https://ngc.nvidia.com/catalog/containers/hpc:namd

Versions

  • 2.13-multinode

  • 2.13-singlenode

  • 3.0-alpha3-singlenode

Commands

  • charmrun

  • flipbinpdb

  • flipdcd

  • namd3

  • psfgen

  • sortreplicas

  • vmd

Module

You can load the modules by:

module load ngc
module load namd

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run namd on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=namd
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml ngc namd