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.
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 environment modules page for more details on the module command.
NAMD may be run by creating a parallel job script (for example, named NAMD_job.com) similar to the following, which will submit the apoa1.namd benchmark model to run on a single 16-core compute node:
#$ -S /bin/bash
#$ -q parallel
#$ -l np=16
module add NAMD/2.12-mp
namd2 +p$NSLOTS apoa1.namd
The script is then submitted for running by typing: