NAMD

Description

NAMD is a high-performance parallel classical molecular dynamics package designed to simulate large biomolecules. Flexible pre and post-processing is made possible through the use of tcl scripts run within VMD. Please see the online documentation for further details.

Modulefile

namd

Documentation

NAMD homepage

Access

Access to NAMD is restricted to those who have read and agreed to the NAMD license. If you wish to use this package, please contact support via email making sure you include your username, name of project leader and a statement indicating that you agree to the terms and conditions of the NAMD license.

Usage

NAMD can efficiently use the underlying communication fabric without an MPI implementation, that is why there are different binaries (and modulefiles) provided for the same version of software: the TCP for Ethernet, the IB for InfiniBand, and a multicore version called SMP.

SMP

Below is an example of a submission script for the multicore version, which can be run at any site. Please note the openmp parallel environment that gets you all the slots on a single host. The maximum number of slots you can request with that parallel environment on our clusters is 16.

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe openmp 4

module load namd/2.9-smp

namd +p$NSLOTS apoa1.namd

TCP

The TCP build is default and can be used at any site. Here is an example of a submission script:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe ompi* 4

module load namd/2.9-tcp

charmrun +p$NSLOTS ++mpiexec ++remote-shell $MPIEXEC $NAMD/namd apoa1.namd

IB

Important

At the present moment we do not recommend using the IB build of NAMD. It will always fail at Fundy and may occasionally fail at Placentia. We discovered that the reason for this is inability of the Charm++ programming system, upon which NAMD relies, to properly detect an active InfiniBand port. We have filed the bug report with Charm++.

Here is an example of a submission script:

#$ -cwd
#$ -l h_rt=01:00:00
#$ -pe ompi 4

module load namd/2.9-ib

charmrun +p$NSLOTS ++mpiexec ++remote-shell $MPIEXEC $NAMD/namd apoa1.namd

Note

• Because NAMD is not a regular MPI application, if you are running the IB build, do not use the wildcard (asterisk) in the name of the ompi parallel environment in order to avoid compute nodes that are not equipped with InfiniBand.