Using FPGA Devices to Accelerate Biomolecular Simulations
Sadaf R. Alam, Pratul K. Agarwal, Melissa C. Smith, Jeffrey S. Vetter, David Caliga · Computer · 2007
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