NAMD with pbs script

From: k.manzoorolajdad (kazem.manzoor_at_gmail.com)
Date: Sun Aug 25 2013 - 09:36:58 CDT

Dear NAMD user:
I use cluster with rock cluster 6 and pbs torque
and see this address
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnPBS
but cant handel
i write the script below:
#!/bin/csh
#PBS -N NAMD
#PBS -k oe
#PBS -m be
#PBS -M kazem.manzoor_at_gmail.com

#set path=(/home/homes53/nbhard2/C2/wrong/namd2 $path .)
cd $PBS_O_WORKDIR

./make-namd-nodelist
./charmrun ./namd2 +p$np ++nodelist ~/namd.$PBS_JOBID MinEqu.conf >&
test.log

and create ./make-namd-nodelist :

#!/bin/sh

nodelist=~/namd.$PBS_JOBID
lists=`cat "$PBS_NODEFILE" | sort`

echo group main > $nodelist
for i in $lists
do
echo host $i >> $nodelist
done

and submit with:
qsub -v np=40 -l nodes=5 namd.pbs

what's my wrong?
thanks
manzoor

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:33 CST