官方网站：
http://www.ks.uiuc.edu/Research/namd/
简介：
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 switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and 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 for biomolecular modeling.
Spotlight: A Molecular Sieve (Jun 2002)
Living cells rely on nutrients absorbed through their cell membranes, for example on glycerol that is key to the cells' metabolism. Proteins, so-called aquaporins, in the membranes form channels that act as sieves permitting passage of water, glycerol, and like molecules, but prevent other molecules of similar size from entry and clogging. For this purpose the channels interact strongly with molecules attempting to pass. In a recent publication, the energetics of the conduction process of glycerol for the aquaporin GlpF was measured in a molecular dynamics simulation, carried out with NAMD, that pulled glycerol through the channel, monitoring the forces needed to advance along the channel axis. An analysis that discounted the irreversible work done on glycerol, a difficult prerequisite, yielded the energy profile that glycerol experiences along the channel and that reflects how the protein decides which molecules are allowed to pass the sieve.
