Kraken will be officially retired and no longer accessible on August 27, 2014. For more information see Kraken Decommission FAQs.
Kraken will be officially retired and no longer accessible on August 27, 2014. For more information see Kraken Decommission FAQs.
The National Institute for Computational Sciences

Nautilus Software

NAMD

Category: Science Apps-Molecular Dynamics

Description

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.

For more information visit NAMD website

Use

NAMD is available on Nautilus as a module. See the modules page for more information on modules.

  module load namd

For runs on large numbers of cores (you will need to experiment) use the following to enable the Charm++ communication thread

namd2 +setcpuaffinity `numactl --show | awk '/^physcpubind/ {printf "+p%d +pemap %d",(NF-2),$2; for(i=3;i<=NF-1;++i){printf ",%d",$i}; print " +commthread +commap",$NF}'` apoa1.namd > logfile

Support

This package has the following support level : Supported

Available Versions

Version Available Builds
intel pgi gnu Other
2.8b3
v