NAMD

Molecular dynamics program

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.

Version

• NAMD 2.6 has been installed on Louhi (louhi.csc.fi)
  
• NAMD version 2.7b1 has been installed on Hippu (hippu.csc.fi) and Louhi (louhi.csc.fi)
  

Usage

Louhi

NAMD scales very well in Louhi. For large systems (100 000 atoms) up to 512 cores can be effectively utilized. Scaling depends on the system and simulation parameters. Thus you should always first check the optimum nuber of processors with small test runs before launching long simulations.

Note that in the queue definitions, the #PBS -l mppwidth= value refers to the number of processor cores to be used.

Below is a sample batch job file, to run NAMD using 128 cores.

#!/bin/sh -l
#PBS -N apoa1
#PBS -r n
#PBS -l mppwidth=128
#PBS -l walltime=05:30:00

cd $PBS_O_WORKDIR
module load namd
aprun -n 128 namd2 namd_config.txt

You can submit the batch queue file with command

qsub namd_job.sh

Hippu

NAMD can be used as a standalone program in hippu.csc.fi.  NAMD starts with commands:

module load namd   
namd2 run_configure_file

If you wish to run NAMD using several processors you must submit the job using charmrun command and explicit path for the namd2 executable. The number of processors to be use is defined with option +p . We recommend that you do not use NAMD in Hippu with more than four processors. All the heavy NAMD simulations, requiring long runs should be executed in Louhi

A sample command for submitting a four processor NAMD job in hippu.

charmrun /v/linux26_x86_64/appl/chem/namd/latest/namd2 +p4 ++local run_configure_file > namd_log &

You can use VMD in Hippu to study and visualize the NAMD results.

Manuals

• NAMD manual

Further information

• NAMD home page.

Reference

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, 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/