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NAMD

Description

NAMD is a molecular dynamics (MD) program designed for parallel computation. Full and efficient treatment of electrostatic and van der Waals interactions are provided via the (O(N Log N) Particle Mesh Ewald algorithm.  NAMD interoperates with CHARMM and X-PLOR as it uses the same force field and includes a rich set of MD features (multiple time stepping, constraints, and dissipatitve dynamics). 

How to Access NAMD

NERSC uses modules to manage access to software. To use the default version of NAMD, type:

% module load namd

To see where the namd executables reside (the bin directory) and what environment variables it defines, type:

% module show namd

E.g., on Cori

% module show namd
-------------------------------------------------------------------
/usr/common/software/modulefiles/namd/20151110: module-whatis NAMD is a scalable parallel molecular dynamics package
prepend-path PATH /usr/common/software/namd/20151110/hsw/bin
-------------------------------------------------------------------

To see the available executables, type:

% ls -l /usr/common/software/namd/20151110/hsw/bin

Using NAMD on Edison and Cori

There are two ways of running NAMD on Cori and Edison: submitting a batch job or running interactively in an interactive batch session. A sample batch script to run NAMD on Edison is:

#!/bin/bash -l
#SBATCH -J test_namd
#SBATCH -p debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_name.o%j

module load namd

srun -n 48 namd2 inputfile >& outputfile

Then submit the job script using the sbatch command, e.g., assume the job script name is test_namd.slurm,

% sbatch test_namd.slurm

To request an interactive batch session, issue a command (e.g., requesting 48 PEs) in your working directory (where your namd inputs are):

% salloc -p debug -N 2

When a new batch session is returned to you, type the following commands:

% module load namd
% srun -n 48 namd2 inputfile >& outputfile

 The same job script would work for Cori. Just note Cori has 32 cores per node, here is the sample job script,

#!/bin/bash -l
#SBATCH -J test_namd
#SBATCH -p debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_name.o%j

module load namd

srun -n 64 namd2 inputfile >& outputfile

 

 


Documentation

More information is available from the Theoretical Biophysics Group at the University of Illinois.

NAMD Online Manual

Availability

PackagePlatformCategoryVersionModuleInstall DateDate Made Default
NAMD cori applications/ chemistry 20151110 namd/20151110 2015-11-24 2015-11-24
NAMD edison applications/ chemistry 2.10 namd/2.10 2015-04-22
NAMD edison applications/ chemistry cvs_01032013 namd/cvs_01032013 2013-01-07 2013-01-07
NAMD edison applications/ chemistry cvs_20130727 namd/cvs_20130727 2013-07-28
NAMD edison applications/ chemistry cvs_20130828 namd/cvs_20130828 2013-08-28
NAMD edison applications/ chemistry cvs_20141119 namd/cvs_20141119 2014-11-19