a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Usage
To list all executables provided by NAMD, run:
$ sbgrid-list namd
Installation
Use the following command to install this title with the CLI client:$ sbgrid-cli install namd Available operating systems: Linux 64, OS X INTEL
Primary Citation*
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J Comput Chem. 26: 1781-1802. (Note: Electronic documents that cite NAMD should also include a link to the NAMD page: http://www.ks.uiuc.edu/Research/namd/)
*Full citation information available through
Citation Note
In addition to using the primary citation listed below, reports or published results obtained with NAMD shall acknowledge its use and credit the developers as: "NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."
Physicist Klaus Schulten once imagined becoming a dancer, relying on nothing but his own mind and body to perform. “But I was not a good dancer,” he says. “So my next thing was theoretical physicist. Just myself, pencil and paper — and in my case, also an eraser.”
That dream was also thwarted. Today, Schulten relies on some of the most powerful and expensive computing equipment on earth to carry out his work, which applies theoretical physics to the understanding of biological systems. His most recent work involved the molecular simulation of an organelle that converts light energy to chemical energy inside a photosynthetic bacterium using the molecular dynamics tools NAMD and VMD, which his lab develops. Looking forward, he wants to simulate an entire living cell, right …
