NAMD

Search Software

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.  Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.

SW Documentation: 
NAMD is best run on the high performance systems where it has been compiled with the latest Intel compilers and recent MPI parallel libraries.  There are different compiled versions of NAMD, which use different parallelization methods.
 

OpenMPI NAMD version

To run this version of software in a Linux environment run the commands:

!/bin/bash -l
#PBS -l walltime=24:0:0
#PBS -l pmem=2gb
#PBS -l nodes=32:ppn=8
module load namd/2.8-ompi
cd $PBS_O_WORKDIR
mpirun namd2 apoa1.namd > apoa1.out 

IBVerbs NAMD version

To run this version of software in a Linux environment run the commands:
#!/bin/bash -l
#PBS -l walltime=0:10:0
#PBS -l pmem=1GB
#PBS -l nodes=4:ppn=8
module load namd/2.8-libverbs
cd $PBS_O_WORKDIR
rm namd.hostfile
for node in `cat $PBS_NODEFILE | sort | uniq`
do
  echo "host ${node}" >> namd.hostfile
done
# Please note there is no line break
# in the following command
charmrun ++remote-shell ssh ++p 32 ++nodelist \ 
namd.hostfile `which namd2` apoa1.namd > apoa1.out

Additional Information

Additional information may be found at: http://www.ks.uiuc.edu/Research/namd
Short Name: 
namd
SW Module: 
namd
Service Level: 
Primary