FPGA-based acceleration of CHARMM-potential minimization
Computer Architecture and Automated Design Laboratory, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215
Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications, HPRCTA ’09
@conference{sukhwani2009fpga,
title={FPGA-based acceleration of CHARMM-potential minimization},
author={Sukhwani, B. and Herbordt, M.C.},
booktitle={Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications},
pages={1–10},
year={2009},
organization={ACM}
}
Energy minimization is an important step in molecular modeling, with applications in molecular docking and in mapping binding sites. Minimization involves repeated evaluation of various bonded and non-bonded energies of a protein complex. It is a computationally expensive process, with runtimes typically being many hours on a desktop system. In the current article, we present acceleration of the energy evaluation phase of minimization using Field Programmable Gate Arrays. We project a multiple orders-of-magnitude speed-up over a single CPU core and a factor of 8 speed-up over our previous acceleration using an NVIDIA Tesla 1060 GPU.
January 3, 2011 by hgpu
