#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=30:00
#PBS -o alanin.out
#PBS -j oe 
#PBS -q	debug 

set -x

# move to directory containing input files
cd  ~/namd

source /usr/share/modules/init/bash

module load namd/2.7


mpirun -np $PBS_NCPUS dplace -s1  namd2 alanin.namd > alanin.log 
 

More on NAMD

Sample jobs

For blacklight

For salk

Documentation

See the NAMD documentation from the University of Illinois at Urbana-Champaign, which includes the User Guide, release notes and information about downloading NAMD to your site.

User Information

PSC Passwords

Connect to PSC systems:

PSC Policies

For technical questions:
Call the PSC hotline: 412-268-6350 / 800-221-1641 or mail to remarks@psc.edu.

Other services PSC provides:

Advanced Networking: High-speed network design, testing and tuning

3ROX: High-speed network access

Biomedical Applications: Computational biomedical research and training