Note: FAQ Database is still being populated.
How do I use namd with the queue on the cluster ?
How do I use namd with the queue on the cluster ?
Association: namd - Posted on: 2006-03-27
Here is an example submit script for running namd on the cluster.
----------------------------------------
#PBS -q max_ecbc
#PBS -N kxt8min
#PBS -l nodes=32:ppn=2
#PBS -W group_list=max_ecbc
------------ Above Normal PBS top -------
export CONV_RSH=ssh
export NODES=`cat $PBS_NODEFILE`
export NODELIST=/tmp/namd2.nodelist
echo group main > $NODELIST
for node in `cat $PBS_NODEFILE`
do
echo host $node >> $NODELIST
done
export N_P=64
/bio/tools/namd/bin/charmrun +p$N_P /bio/tools/namd/bin/namd2 ++nodelist
$NODELIST /bio/data/genomics/agarrett/md/1kxt/namd/8namd-min.inp >
/bio/data/genomics/agarrett/md/1kxt/namd/8min.out
