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 Hopper,

% module show namd           (or type module show namd/2.9)

-------------------------------------------------------------------
/usr/common/usg/Modules/modulefiles/namd/2.9:

module-whatis     NAMD is a scalable parallel molecular dynamics package 
prepend-path     PATH /usr/common/usg/namd/2.9/bin 
-------------------------------------------------------------------

To see the available executables, type:

% ls -l /usr/common/usg/namd/2.9/bin

Using NAMD on Hopper

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

#PBS -N test_namd
#PBS -q debug
#PBS -l mppwidth=48
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load namd

aprun -n 48 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 48 PEs):

% qsub -I -V -q interactive -l mppwidth=48

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

% cd $PBS_O_WORKDIR
% module load namd
% aprun -n 48 namd2 inputfile >& outputfile

Running NAMD replica exchange simulations on Hopper

NAMD 2.9 has changed the way lauching replica jobs and therefore the replica jobs run in the Hopper native enviornment.  The sample job script is as follows:

#PBS -S /bin/csh
#PBS -N test_replica
#PBS -q debug
#PBS -l mppwidth=96,walltime=00:30:00
#PBS -j oe

cd $PBS_O_WORKDIR

module load namd/2.9

make_output_dirs.sh output  8
aprun -n 96 namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
aprun -n 96 namd2 +replicas 8 job1.conf +stdout output/%d/job0.%d.log
#See the directory for an example, /global/common/hopper/usg/namd/2.9/lib/replica/example

If you use NAMD 2.8 you have to run the replica exchange jobs under the Cluster Compatiblity Mode (CCM) on Hopper. Because Hopper native environment doesn't support the socket operations between compute nodes, which are needed for the commnication between replicas. 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

Please note, NAMD 2.9 has changed the way lauching replica jobs, the sample job script is as follows:

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

cd $PBS_O_WORKDIR

module load namd/2.9

make_output_dirs.sh output  8
mpirun -n 64 namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
mpirun -n 64 namd2 +replicas 8 job1.conf +stdout output/%d/job0.%d.log
#See the directory for an example, /global/common/carver/usg/namd/2.9/lib/replica/example

To run NAMD replica jobs on Carver using namd/2.8 (and earlier versions), 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