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 following versions are installed and currently available...

... on environment hpc-env/8.3:

• NAMD/2.14-fosscuda-2019b
• NAMD/2.15alpha1_2021-07-22-fosscuda-2019b
• NAMD/3.0alpha8-fosscuda-2019b-multicore-CUDA-SingleNode
• NAMD/3.0alpha8-fosscuda-2019b-netlrts-smp-CUDA-SingleNode

... on environment hpc-env/6.4:

• NAMD/2.13-intel-2018a-mpi
• NAMD/2.13-verbs

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

which will load the most recent version of NAMD available in the current environment.

License

NAMD is licensed software provided by the Theoretical and Computational Biophysics Group (TCBG) of the University of Illinois. The official license can be found online and in the installation directory:

 module load NAMD
 less $EBROOTNAMD/license.txt

The software NAMD can be used as-is and free of charge for research. By using the provided installation of NAMD on our HPC cluster, you agree to abide by the terms of the license. In particular, you should acknowledge the use of NAMD and cite the appropriate papers (see below) in your publications.

Documentation

The full documentation of NAMD can be found here.

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