Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations

• Published in: 2006 International Conference on Field Programmable Logic and Applications pp. 1 - 8
• Main Authors: Yongfeng Gu, VanCourt, T., Herbordt, M.C.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.01.2006
• Subjects: Acceleration; Biochemistry; Computational modeling; Field programmable gate arrays; Interpolation; Life estimation; Particle accelerators; Pipelines; Technological innovation; Testing
• ISBN: 9781424403127; 142440312X
• ISSN: 1946-147X
• DOI: 10.1109/FPL.2006.311190

FPGA-based acceleration of molecular dynamics (MD) has been the subject of several recent studies. The paper describes a new non-bonded force computation pipeline implemented on a 2004-era COTS FPGA board and its integration into the ProtoMol MD code. There are several innovations: a novel interpolation strategy; the introduction of a "semi-floating point" format; and various issues related to system integration. As a result, the authors are able to model far more particle types, without relying on complex buffering, and obtain higher accuracy than previously. A two pipeline accelerator has been implemented on a Xilinx VirtexII Pro VP70, integrated into ProtoMol, and tested with an enzyme inhibitor model having 8000 particles and 26 particle types. Despite performing all O(n) work on the host PC, as well as the data conversion and communication overhead, this implementation yields a 5.5times speed-up over a 2.8GHz PC, and with accuracy comparable to the serial code