NAMD - Scalable Molecular Dynamics

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Parallel Programming Laboratory

Bionumerics Research Group

NAMD, recipient of a 2002 Gordon Bell 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 processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. 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. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

NAMD reference paper: Scalable molecular dynamics with NAMD.

Other Spotlights

Spotlight: Closing the Gaps (April 2009)

NCSA News Release: Biophysicists at the University of Pennsylvania used NAMD running on NCSA's Abe to clarify a mysterious interaction between cholesterol and neurotransmitter receptors. Research into how anesthesia works may eventually unlock not only that mystery but dozens of others as well. "Anesthetics have improved significantly over the last hundred years, but the mechanism of anesthesia is not understood at all," says Grace Brannigan, a researcher at the University of Pennsylvania's Center for Molecular Modeling (CMM).

To gain insight into how anesthetics work, a team consisting of Brannigan and fellow researcher Jérôme Hénin, University of Pennsylvania professors Michael Klein and Roderic Eckenhoff, and Richard Law of the Lawrence Livermore National Laboratory, is focusing on the nicotinic acetylcholine receptor (nAChR). This receptor, found in both brain and muscle cells, is a ligand-gated ion channel. The channel opens or closes in response to binding with a chemical messenger (ligand) such as a neurotransmitter, like acetylcholine. When the channel is open, ions can cross the membrane. Anesthetics are believed to close the channel, thus reducing sensations and possibly causing the memory loss associated with being under general anesthetic.

The researchers hope their work leads to improved drug design. "You could fine-tune the properties of the drug if you could understand how the mechanism works," says Brannigan. "For instance, by understanding how anesthetics work, you could design new anesthetics that could be more powerful yet maybe wouldn't have some of the side effects that current ones do."

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Spotlight: Closing the Gaps (April 2009)

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