NAMD - Molecular dynamics

NAMD, a package to perform molecular dynamics, is available on Lisa.

Usage (old package)

  • NAMD is available with the command:
module load namd/64 c/intel openmpi fftw2/openmpi/intel/64/2.1.5sp

Look at this page how to run parallel programs.

  • NOTICE: To be able to use NAMD you have to contact our helpdesk (hic@surfsara.nl) and request to be added to the group "namd".

Usage (new package)

  • NAMD is available with the command:
module load namd/2.7

Running namd2

This is an example job, using 2 nodes and making use of the module saranodes. This module creates a nodefile which enables you to use all cores available.

#PBS -lnodes=2 -lwalltime=1:00:00
module load namd/2.7 saranodes
np=$(wc -l < $SARA_NODEFILE)      # this gives the total number of cores available
nodefile=$(tempfile)
cat $SARA_NODEFILE | sed 's/^/host /' > $nodefile # this creates a suitable nodefile
if [ "$(ls -A /sys/class/infiniband 2>/dev/null)" ] ; then
  sed -i "s/gb/ib/" $nodefile    # use ib interface if available
fi
cd $HOME/workdir
charmrun ++nodelist $nodefile +p$np $(which namd2) test.namd