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: Amazing Filter (April 2009)

image size: 504.2KB
movie: 8.7MB
made with VMD

Many living cells, so-called eukaryotic ones, organize their genetic materials in the cell's nucleus, enveloped by a double membrane with guarded access through pores that involve an amazing filter. Like an ordinary filter it permits passage of small particles (biomolecules), but not of large particles (e.g., proteins). However, certain large particles, proteins called transport receptors, can pass. The filter is made of long "finger" proteins anchored inside the pores. The transport receptors can intermittently widen the filter. But to observe how this is achieved is difficult since the finger proteins are highly disordered. As reported recently, simulations using NAMD suggest now a simple and elegant answer: the finger proteins bundle in groups of 2 - 6 and form a brush, filling with its bristles the nuclear pores. The bristles are bundles of finger proteins and have two key properties: (i) on their surface they are dotted with spots of amino acid pairs, phenylalanine and glycine, that are known to interact favorably with transport receptors (see the Aug 2007 highlight, the Feb 2007 highlight, and the Jan 2006 highlight); (ii) the bristles are also interconnected, namely where finger proteins change from one bundle to another bundle, which they do with some frequency. It appears then that the bristles of the nuclear pore filter form an energetically favorable environment for transport receptors and that the latter can tear a finger protein readily away from a bundle to form a wider space for passage. More information here.

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Spotlight: Amazing Filter (April 2009)

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