NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. The software is developed and distributed by the Theoretical and Computational Biophysics Group at the Beckman Institute of the University of Illinois.

Available

Puhti: version 2.13

License

CSC has obtained a Computing Centre license, which allows usage for non-commercial research. For commercial use, contact (namd@ks.uiuc.edu) See also acknowledging usage below.

Usage

NAMD developers recommend to use one core per task for communication, but sometimes using all cores for computing can give a little better performance. Please test with your input. Make sure the "number tasks per node" times "cpus per task" equals 40, i.e. all cores in a node. Try different ratios and select the optimal one.

This script would use 2 tasks per node, 20 cores per task, and one of them for communication, using two full nodes, i.e. 80 cores.

#!/bin/bash 
#SBATCH --partition=test
#SBATCH --nodes=2             
#SBATCH --time=0:06:00        
#SBATCH --account=<project>
#SBATCH --ntasks-per-node=2  # test to find the optimum number, 2-40
#SBATCH --cpus-per-task=20   # 40/(ntasks-per-node)

module load namd

# NAMD suggests using 1 thread per task for communication
# using all cores for computing may still be faster

(( namd_threads = SLURM_CPUS_PER_TASK - 1))

# one core per task for communication
srun -n ${SLURM_NTASKS} namd2 +ppn $namd_threads +isomalloc_sync apoa1.namd  > apo1.out

# all cores for computing
#srun -n ${SLURM_NTASKS} namd2 +ppn ${SLURM_CPUS_PER_TASK} +isomalloc_sync apoa1.namd  > apo1.out

Submit the batch job with:

sbatch namd_job.bash

References

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."

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal

In addition, electronic documents should include the following link: http://www.ks.uiuc.edu/Research/namd/

More information

NAMD manual

NAMD home page.