how to run namd in cluster

From: Anupam Nath Jha (
Date: Sun Jul 27 2008 - 13:23:22 CDT

Dear all
I have installed namd in our cluster (x86_64) and when i am trying to run it by
following script file:

#This is a PBS script for Parallel Jobs
#!/bin/bash -f
#PBS -o /home/anupam/NAMD
#PBS -e /home/anupam/NAMD
#PBS -q default
#PBS -l nodes=1:ppn=4

cd /home/anupam/NAMD

mpiexec -machinefile $PBS_NODEFILE -np 4 namd2 ubq_ws_eq.conf

but it's not doing anything and saying :
problem with execution of namd2

whereas namd is installed and set as command

what am I doing wrong?

thanks with regards

Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.
Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
Ph. no.-22932611
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