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NAMD

NAMD

Description

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

Version on CSC's Servers

Taito: 2.9, 2.11 (also GPU), 2.13


Usage

FGI Grid

Taito

Below is a sample batch job file, to run NAMD using 96 cores using full nodes. Always test for efficient scaling first!

#!/bin/bash -l
#SBATCH -t 00:10:00
#SBATCH -p parallel
#SBATCH -J NAMD
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=24
#SBATCH --mail-type=END
##SBATCH --mail-user=your.name@yourinstitute.fi # uncomment to receive email

module load namd-env/2.13

srun namd2 alanin > alanin.out

You can submit the batch queue file with command

sbatch namd_job.bash

Note that namd2 is also available in taito-shell.csc.fi which allows currently interactive usage upto 8 cores.


Discipline

Biosciences
Chemistry

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/

 


Support

servicedesk@csc.fi


Manual

NAMD manual

NAMD home page.