NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Official homepage: www.ks.uiuc.edu/Research/namd/

Installations on NSC systems

Tetralith and Sigma

NAMD is available via the module system on Tetralith and Sigma. For more information about available versions, please see the Tetralith and Sigma Software list.

How to run

A simple batch script:

  #!/bin/bash
  #SBATCH -n 32
  #SBATCH -t 12:00:00
  #SBATCH -J jobname
  #SBATCH -A SNIC-xxx-yyy

  ml namd/2.12-nsc1-intel-2018a-eb
  mpprun namd2 your_inputfile.namd > output.txt