HIGH PERFORMANCE SOFTWARE FOR BIOMOLECULAR DYNAMICS

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This award addresses the need for less time-consuming simulations of larger biomolecular systems, for example water-membrane systems of more than ten thousand atoms. The recent availability of implementations of the three-dimensional fast multipole method presents an opportunity for the rapid implementation of enhancements to a molecular dynamics package. Highly suitable is a computer program of the investigator and his collaborators called MD, which interfaces to the data files and processing routines of a popular macromolecular modeling package. The program MD has been used to test computational methods, to advance science, and to benchmark computer systems. The PI will incorporate code into MD that implements the fast multipole method, will parallelize this code, and will combine it with distance class techniques and simple higher order time-integrated schemes.