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 Franklin,

% module show namd           (or type module show namd/2.6)
-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/namd/2.6:

module-whatis	 Molecular dynamics simulations 
module-whatis	 loads the namd suite 
prepend-path	 PATH /usr/common/usg/namd/2.6/bin 
prepend-path	 MANPATH /usr/common/usg/namd/2.6/man 
-------------------------------------------------------------------

To see the available executables, type:

% ls -l /usr/common/usg/namd/2.6/bin

Using NAMD on Franklin and Hopper

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

#PBS -N test_namd
#PBS -q debug
#PBS -l mppwidth=32
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load namd

aprun -n 32 namd2 inputfile >& outputfile 

Then submit the job script using theqsub command, e.g., assume the job script name is test_namd.pbs,

% qsub test_namd.pbs

To request an interactive batch session, issue a command (e.g., requesting 32 PEs):

% qsub -I -V -q interactive -l mppwidth=32

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

% cd $PBS_O_WORKDIR
% module load namd
% aprun -n 32 namd2 inputfile >& outputfile

Running NAMD replica exchange simulations on Hopper

NAMD replica exchange simulation coudln't run on Hopper in the past due to the lack of the socket operations needed for the communicate between replicas . With the rencent availability of  Cluster Compatibility Mode (CCM) on Hopper, the NAMD replica exchange jobs can run on Hopper now. Please refer to our website for more information about CCM.

To run NAMD replica jobs under Hopper CCM, please copy the tcl scripts in the directory /usr/common/usg/namd/2.8_ccm/bin/replica_ccm into your working directory, and submit job script as follows:

#PBS -S /bin/csh
#PBS -N test_replica
#PBS -q ccm_int 
#PBS -l mppwidth=120,walltime=00:30:00
#PBS -j oe

cd $PBS_O_WORKDIR

module load ccm
setenv CRAY_ROOTFS DSL

ccmrun tclsh ./replica_exchange.tcl myexample.conf

Using NAMD on Carver

A sample batch script for Carver:

#PBS -l nodes=2:ppn=8,walltime=0:30:00
#PBS -N test_namd 
#PBS -j oe 
#PBS -q debug
#PBS -V

cd $PBS_O_WORKDIR

module load namd
mpirun -np 16 namd2 inputfile >& outputfile  

Running NAMD replica exchange simulations on Carver

To run NAMD replica jobs on Carver, please copy the tcl scripts in the directory /usr/common/usg/namd/2.8/bin/replica into your working directory, and submit job script as follows:

#PBS -S /bin/csh
#PBS -N test_replica 
#PBS -l nodes=4:ppn=8
#PBS -l walltime=30:00
#PBS -q debug 
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR

tclsh ./replica_exchange.tcl myexample.conf

Examples

Small alpha helix 12 residues (66 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Execute: namd2 alanin.conf > output

DNA peptide complex 11254 residues, 11040 waters (36573 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Forcefield files
• Execute: namd2 er-gre.namd > output

Alpha Lipo-protein A 22010 residues, 21458 waters (92224 atoms)

• Config file
• PDB Structure file
• PSF Structure file
• Forcefield files
• Execute: namd2 apoa1.namd > output

Documentation

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

NAMD Online Manual

Availability