NAMD

License Arrangements

This software is installed with a non-commercial use license. Access to this software is restricted. User must agree to the license, found here. Please send a written statement accepting the license terms as a ticket to the Research Computing Team (https://bit.ly/arc-help) in order for us to give you access to NAMD.

Example submission script

An example script, namdexample.sh , looks like:


#!/bin/bash
#$ -pe ib 8
#$ -l h_rt=12:0:0
#$ -l h_vmem=1G
#$ -cwd

module add namd/2.9
mpirun namd2 name_of_config_file.conf > output_log_file.log

This example requests 8 cores for 12 hours, with each core limited to 1Gb of RAM. It assumes that you are submitting the job from the directory containing your input files.

Note: prior to NAMD 2.9, the namd2 binary was called namd2.MPI .