NAMD


Level of support

Tier 2 NSC has only limited experience with this software, but we will try to help as much as possible. We have ran some tests, for example, if the program comes with a test suite, but they may be far from exhaustive. We will try to install and test new versions, as soon as we can.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Official homepage: www.ks.uiuc.edu/Research/namd/

The NAMD 2.9 user guide is available online at www.ks.uiuc.edu/Research/namd/2.9/ug/

Please contact NSC Support if you have any questions or problems.

How to run

Example batch script:

#!/bin/bash 

#SBATCH --time=10:00:00                #Requested walltime 
#SBATCH --nodes=2 --exclusive          #Number of compute nodes to allocate
#SBATCH --account=liu-2012-00060-20    #Account string for the project that you wish to account the job to

module load namd/2.12

#Run namd. mpprun is NSC specific and sets up the parallel computation.
mpprun namd2 your_inputfile.namd > output.txt

exit 0
#END OF SCRIPT

Note that you must edit the account string, walltime and number of requested nodes before submitting!