3 NVIDIA Grace-Hopper nodes (GH200 480) are now available. See Using Bede for more information.



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.