TCBG Seminar

Scalable Algorithms for Fast Molecular Dynamics Simulation and Elucidation of Protein Function

Dr. Ron Dror
D. E. Shaw Research
New York, NY

Monday, October 8, 2007
3:00 pm (CT)
3269 Beckman Institute


Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. Such events include functionally important changes in protein structures, folding of proteins to their native three-dimensional structures, and interactions between proteins or between proteins and candidate drug molecules. We have developed several new algorithms that significantly accelerate parallel MD simulations compared with current state-of-the-art codes. These methods are embodied in an MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. For example, on a standard benchmark, Desmond’s performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM’s Blue Gene/L machine with 32K processors running its Blue Matter MD code. The ability to perform long MD simulations quickly has allowed us to provide an atomically detailed explanation for the mechanisms of several proteins, such as the sodium-proton antiporter NhaA.

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