NAMD

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

Installed versions

  • NAMD 3.0b3 (default, Linux-x86_64-multicore-CUDA)

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

Submitting a NAMD calculation

This module load command is needed once per session:

module load namd3

TO demonstrate the NAMD job submission, the steps and the four necessary files are given below for a minimalistic NAMD minimization calculation

  1. The NAMD input file minim.namd:

# ===== AMBER =====
amber           on
parmfile        water5.prmtop      ;# AMBER topology
ambercoor       water5.inpcrd      ;# AMBER coordinates

# AMBER compatible 1-4
exclude         scaled1-4
1-4scaling      0.833333           ;# ~1 / 1.2 (AMBER SCEE)
scnb            2.0                ;# AMBER default SCNB

# ===== PBC =====
cellBasisVector1    29.637   0.0     0.0
cellBasisVector2     0.0    29.980   0.0
cellBasisVector3     0.0     0.0    28.185
cellOrigin           0.0     0.0     0.0

wrapAll         on

# ===== PME =====
cutoff          8.0
switching       on
switchdist      7.0
pairlistdist    10.0

PME             yes
PMEGridSpacing  1.0

# ===== MD =====
timestep        2.0
temperature     300

# ===== OUTPUT =====
outputName      min
binaryoutput    yes

outputEnergies  50
outputPressure  50
restartfreq     500

# ===== MINIMIZATION =====
minimize        500

The necessary coordinate (water5.inpcrd) and topology (water5.prmtop) file can be accessed from here:

  1. water5.inpcrd

  2. water5.prmtop

  3. Job script for a regular NAMD SLURM job (subNAMD.sh):

#!/bin/bash
#SBATCH -J NAMD3
#SBATCH -t 01:00:00
#SBATCH -p gpu
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16

module purge
module load PrgEnv-gnu/8.3.3
module load gcc/12.2.0
module load cray-mpich/8.1.24
module load cray-libsci/23.09.1.1
module load namd3

srun namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll +devices 0 +setcpuaffinity minim.namd > minim.out

Then to submit the NAMD job via SLURM to the KOMONDOR gpu queue:

sbatch subNAMD.sh

How to Cite NAMD

The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:

“NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.”

Any published work which utilizes NAMD shall include the following reference:

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid. Scalable molecular dynamics on CPU and GPU architectures with NAMD. Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475 https://pubs.aip.org/aip/jcp/article-abstract/153/4/044130/1064953/Scalable-molecular-dynamics-on-CPU-and-GPU?redirectedFrom=fulltext

Last update by Milán SZŐRI: 2025-12-03