NAMD

Introduction

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, 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. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

Installed version

The currently installed version of NAMD on the cluster is 2.12.

Using NAMD on the HPC cluster

If you want to use NAMD on the Cluster, you will have to load the corresponding module first. You can do that by using the command:

module load NAMD

Documentation

The full documentation of NAMD can be found here.

Instructions on how to cite NAMD and papers can be found here.