NAMD

A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Installed versions:

NAMD 3.0b3 (default, recommended)

NAMD manual can be downloaded from here: https://www.ks.uiuc.edu/Research/namd/3.0/ug/

Submitting a NAMD calculation

This ‘source’ command is needed once per session:

module load namd3

This commands is equivalent to:

module load namd3/smp-CUDA

Example job script for a regular NAMD SLURM job looks like this:

#!/bin/bash
#SBATCH -A XXXX-XX-XX
#SBATCH -J namdjob
#SBATCH -t 00:10:00
#SBATCH --nodes=2
#SBATCH -p main
#SBATCH --ntasks-per-node=128
# load the NAMD module
ml PDC/<version>
ml NAMD/3.0b
# Run namd

srun namd3 input.namd > output_file

Last update by Milán SZŐRI: 2025-05-12