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The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle lead to important scientific advances and provide a powerful new tool for drug discovery. A wide range of biologically important processes, however, occur over time scales on the order of a millisecond ~ several orders of magnitude beyond the duration of the longest previous MD simulations. Our research group has completed a specialized, massively parallel machine called Anton, which is capable of calculating millisecond-scale molecular trajectories at an atomic level of detail. The machine has greatly extended the power of simulation as a tool for understanding the structure and dynamics of proteins, and has already allowed us to observe and analyze important biological phenomena that have not previously been accessible to either computational or experimental study.