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 |
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