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NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

  • Version: 2.13b
  • Machines: Clusters with InfiniBand network
  • Location: /uufs/chpc.utah.edu/sys/installdir/namd

Information:

To get details of the functionality of VMD visit the website: http://www.ks.uiuc.edu/Research/namd/

To Use:

The builds that we provide have support the InfiniBand network through the ibverbs interface. NAMD uses charm++ parallel objects for parallelization and as such the program launch uses the charmrun interface. One also has to create a specific host file that lists the nodes on which to run.

SLURM script written in tcsh needs to include the following:

#load NAMD module
module load namd
set NAMD2_FULLPATH = `which namd2`

# prepare hostfile for charmrun
srun hostname | sort > nodefile
echo group main > hostfile
set NODES = `cat nodefile`
foreach node ( $NODES )
echo host $node >> hostfile
end
set PROCS = `cat nodefile | wc -l`

# run NAMD via charmrun, using input file input.namd
setenv in input
charmrun $NAMD2_FULLPATH +p$PROCS ++nodelist hostfile +setcpuaffinity $in.namd > $in.log
Last Updated: 9/18/18