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 .