Highlights of our Work
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made using VMD
The computer processor is the workhorse of biomolecular modeling, with NAMD the plow to which a single processor or a team of thousands may be hitched. The recent release of NAMD 2.6 has extended the drawbar to harness the power of several thousand processors: 2000 on a Cray XT3 and 8,000 on an IBM Blue Gene/L. This permits the efficient simulation of an entire ribosome, the cell's protein factory, comprising 3,000,000 atoms when solvated. But the features and increased performance of NAMD 2.6 are also available to the scientist with only a laptop, on which a domain of the muscle protein titin (10,000 atoms solvated) can be readily simulated. NAMD has also become more versatile, supporting more force fields (OPLS, CHARMM with CMAP cross terms), calculating free energies, and executing customizable replica exchange simulations. In addition, NAMD can now be called from the structure analysis program VMD to calculate, for example, interaction energies between protein domains. Like increased horsepower in transportation, increased simulation power opens new routes, routes to study entire systems of biopolymers like the ribosome, not just one piece.