NAMD#
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 cores for typical simulations and beyond 500,000 cores for the largest simulations.
On Bede, NAMD is made available through the HECBioSim Project.
# Load the hecbiosim project
module load hecbiosim
# Load the desired version of namd
module load namd
module load namd/2.14-smp
module load namd/3.0-alpha12-singlenode
module load namd/3.0-alpha9-singlenode
For more information see the NAMD User’s Guide.