Paper Citing NAMD - Abstract
Gu, Y.; VanCourt, T.; Herbordt, M.C.
Accelerating molecular dynamics simulations with configurable circuits
IEE PROCEEDINGS-COMPUTERS AND DIGITAL TECHNIQUES, 153:189-195, MAY 2006
Molecular dynamics (MD) is of central importance to computational chemistry. Here the authors show that MD can be implemented efficiently on a commercial off-the-shelf (COTS) field programmable gate array (FPGA) board, and that speed-ups from 31 x to 88 x over a PC implementation can be obtained. Although the extent of speed-up depends on the stability required, 46x can be obtained with virtually no detriment, and the upper end of the range is apparently viable in many cases. The authors sketch the FPGA implementations and describe the effects of precision on the trade-off between the performance and quality of the MD simulation.
