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.
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!