The NAMD molecular dynamics simulator

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. The current version available on the HEC is the multi-threaded version, which can run in parallel using cores on the same compute node, similar to the OpenMP model of parallelism (read more about OpenMP on the Using OpenMP on the HEC page).

To access the default version of NAMD on the HEC, simply type the command:

module add NAMD

To see what other versions of NAMD are currently available, type:

module avail NAMD

See the Using environment modules on the HEC page for more details on the module command.

A sample parallel job script for NAMD

NAMD may be run by creating a parallel job script (for example, named similar to the following, which will submit the model in input file Efield_1.inp to run on 16 cores:


#SBATCH -p parallel
#SBATCH --cpus-per-task=16
#SBATCH --mem=1G

source /etc/profile
module add NAMD/2.12-mp

namd2 +p${OMP_NUM_THREADS} Efield_1.inp > Efield_1.log

The script is then submitted for running by typing:


Further Reading

The NAMD Home Page