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NAMD

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

  • Version: 2.14
  • 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/

We have the smp cpu version (ml namd/2.14.verbs-smp) as well as a GPU build (ml namd/2.14.verbs-smp-CUDA)

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.

the SLURM script written in tcsh needs to include the following:


#load NAMD module
module load namd/2.14.verbs-smp
set NAMD2_FULLPATH = `which namd`

#set up hostfile
srun hostname | sort > nodefile
echo group main > hostfile
set NODES = `cat nodefile`
foreach node ( $NODES )
 echo host $node >> hostfile
end

# run NAMD via charmrun, substituting in your input and output file names
charmrun $NAMD2_FULLPATH ++ppn $SLURM_NTASKS ++nodelist hostfile ubq_ws.namd > ubq_ws.log
Last Updated: 6/10/21