Namd

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. NAMD is distributed free of charge with source code.

Usage

Example script : testNamd.sh

#!/bin/bash
#SBATCH --job-name=alanin
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --mem=32G
#SBATCH --time=1-00:00:00
#SBATCH --partition=thin
#

module load namd/3.0b6

namd3 +p ${SLURM_TASKS_PER_NODE} alanin.conf > alanin.log

Example files can be found at : lib/replica/example/ in NAMD_3.0_Linux-x86_64-multicore.tar.gz

Submit with :

sbatch --account=your_project_ID testNamd.sh

More info :

• https://www.hpc.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:userguide:namd
• https://www.ks.uiuc.edu/Research/namd/2.8b2/ug.pdf