[edit] NAMD on the ITS HPC Cluster

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Version 2.6 is currently available on the Case HPC cluster.

Proper environment setting for use of NAMD is contained in the "namd-2.6-amd64-tcp" module, conveniently aliased to simply "namd":

   module load namd

To run a NAMD batch job on the cluster, you need to create a PBS script. The sample script below includes a request for two single-core 3.8 GHz processors in each of two compute nodes on the Gigabit Ethernet interconnect and imposes a limit of 10 hours of wall time. Note that the script includes the commands to load the required modules in order to correctly set the environment of the batch job.

  #PBS -N namd_test
  #PBS -l walltime=10:00:00
  #PBS -l nodes=2:ppn=2:single3800
  #PBS -j oe
  #
  # Load the NAMD and MPICH1 modules
  module load namd
  module load mpich1
  #
  # cd to the directory where the job was submitted
  cd $PBS_O_WORKDIR
  #
  # Run NAMD
  run_namd input.file

In the above sample script, note that 'input.file' should be replaced by the name of your input file containing NAMD commands to be carried out.

For more information, including tutorials on how to use NAMD and VMD for biomolecular modeling, see the official NAMD web site at the University of Illinois at Urbana-Champaign.

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