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Using FPGA Devices to Accelerate Biomolecular Simulations

2007; IEEE Computer Society; Volume: 40; Issue: 3 Linguagem: Inglês

10.1109/mc.2007.108

1558-0814

Sadaf R. Alam, Pratul K. Agarwal, Melissa C. Smith, Jeffrey S. Vetter, David Caliga,

Protein Structure and Dynamics

A field-programmable gate array implementation of a molecular dynamics simulation method reduces the microprocessor time-to-solution by a factor of three while using only high-level languages. The application speedup on FPGA devices increases with the problem size. The authors use a performance model to analyze the potential of simulating large-scale biological systems faster than many cluster-based supercomputing platforms