FPGA-accelerated molecular dynamics simulations: an overview

Authors:
Xiaodong Yang;Shengmei Mou;Yong Dou
Affiliations:
School of Computer Science, National University of Defense Technology, Changsha, P.R. China;School of Computer Science, National University of Defense Technology, Changsha, P.R. China;School of Computer Science, National University of Defense Technology, Changsha, P.R. China
Venue:
ARC'07 Proceedings of the 3rd international conference on Reconfigurable computing: architectures, tools and applications
Year:
2007

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Abstract

Molecular Dynamics (MD) simulation, supported by parallel software and special hardware, is widely used in materials, computational chemistry and biology science. With advances in FPGA capability and inclusion of embedded multipliers, lots of studies steer to focus on FPGA-accelerated MD simulations. In this paper we make an overview on the background of MD simulations and latest FPGA-based research programs. Characteristics, major approaches and problems are introduced, and possible solutions are also discussed. Finally, some future directions of research are given.