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Interactive Molecular Dynamics

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Olga Svinarski and VMD
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The import of material into biological cells needs to be highly selective. Which physical interactions are the best capable of differentiating suitable from unsuitable imports? How can one keep import traffic fast despite strong selection? As one knows from border crossing, fast traffic and high security can be conflicting objectives. A recent investigation employed a new simulation method to answer the above questions for import of glycerol through a membrane channel. Linking the renown molecular graphics program VMD with the simulation program NAMD permits researchers to view "live" proteins, e.g., the membrane channel, and employing computer game technology, namely, a device that permits one to pull glycerol through the simulated channel, researchers can feel the mechanical resistance of the pulled glycerol, guide it through the channel, and directly observe the selection process involving glycerol's shape, capability for hydrogen bonding, and electric dipoles. The new methodology, interactive molecular dynamics, will revolutionize computational biology and is one of the first tools that take advantage of fast (TeraGrid) computer networks in linking local graphics workstations (running VMD) with a distant supercomputer (running NAMD). The method has received an enthusiastic editorial comment.