FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.

中文翻译：

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用于分子动力学模拟中短程力计算的基于 FPGA 的协处理器的显式设计。

基于 FPGA 的分子动力学模拟 (MD) 加速已成为最近几项研究的主题。主导执行时间的短程力计算是主要焦点。在这里，我们结合了：高级别的 FPGA 特定设计，包括单元列表、系统确定的插值和精度、排除处理以及对高达 256K 粒子的 MD 模拟的支持。目标系统由带有 2004 年 COTS FPGA 板的标准 PC 组成。有几项创新：几个主要组件的新微架构，包括单元列表处理器和片外存储器控制器；和一种新颖的算术模式。需要进行大量实验来优化精度、插值顺序、插值模式、表格大小和模拟质量。