Efficient Calculation of Pairwise Nonbonded Forces

Matt Chiu, Md. Ashfaquzzaman Khan, Martin C. Herbordt
Department of Electrical and Computer Engineering, Boston University, Boston, MA
IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), 2011


   title={Efficient Calculation of Pairwise Nonbonded Forces},

   author={Chiu, M. and Khan, M. and Herbordt, M.C.},

   booktitle={Field-Programmable Custom Computing Machines (FCCM), 2011 IEEE 19th Annual International Symposium on},





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A major bottleneck in molecular dynamics (MD) simulations is the calculation of the pair wise nonbonded interactions. Previous work on FPGAs has shown that these calculations can be implemented with a number of force computation pipelines operating in parallel (4 and 8 for the Stratix-III and Stratix-V, respectively). Optimization has received some attention previously in CPU, GPU, FPGA, and ASIC implementations, with direct computation of the equations of interaction being replaced with table lookup with interpolation, and the order and granularity of those interpolations being optimized. FPGAs lend themselves to a particularly rich design space both of opportunities and constraints. We explore and evaluate this space with respect to both resource requirements and simulation quality. We find that FPGAs’ BRAM architecture makes them well suited to support unusually fine-grained intervals. This leads to a reduction in other logic and a proportional increase in performance. We demonstrate these designs with prototype implementations supporting full electrostatics and integrated into NAMD-lite. Throughput is improved by 50% over the previous best FPGA implementation while simulation quality is maintained.
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