Description

Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation.

More information

- Homepage: http://www.ks.uiuc.edu/Research/namd

Available Versions of NAMD

Version	Module	Available on

Version	Module	Available on
3.0alpha13-multicore-CUDA-SingleNode	chem/NAMD/3.0alpha13-multicore-CUDA-SingleNode	Noctua 2

This table is generated automatically. If you need other versions please click pc2-support@uni-paderborn.de.

Usage Hints for NAMD

If you need support in using this software or example job scripts please click pc2-support@uni-paderborn.de.

Usage on Noctua 2

#!/bin/bash
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=32
#SBATCH --partition=gpu
#SBTACH --gpus-per-task=1
#SBATCH --gres=gpu:a100:1
#SBATCH -t 2:00:00

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

module reset
module load chem/NAMD/3.0alpha13-multicore-CUDA-SingleNode
srun namd3 +p1 +setcpuaffinity --CUDASOAintegrate on +devices 0 input.namd