NAMD

Software description

NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. 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.

Simple job script example

#!/bin/bash

#SBATCH --time=120
#SBATCH --ntasks=64
#SBATCH --account=naiss202X-Y-ZZ

module load NAMD/3.0b5-hpc1-gcc-11.3.0-bare

mpprun namd3 jag_input_file.namd &

Available Modules

3.0b5-hpc1-gcc-11.3.0-bare

Load with:

[user@system ~]$ module load NAMD/3.0b5-hpc1-gcc-11.3.0-bare