最近看到一篇关于硬件加速分子动力学模拟的JCTC文章 Accelerators for Classical Molecular Dynamics Simulations of Biomolecules ，对比了图形处理器GPU、现场可编程逻辑门阵列 FPGA、专用集成电路ASIC应用于分子动力学模拟加速。本文对各种硬件有易于理解的介绍，可供入门了解学习硬件加速高性能计算。
论文地址：10.1021/acs.jctc.1c01214
论文摘要：
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model biomolecular structures such as proteins and their interactions with drug-like small molecules with greater spatiotemporal resolution than is otherwise possible using experimental methods. MD simulations are notoriously expensive computational endeavors that have traditionally required massive investment in specialized hardware to access biologically relevant spatiotemporal scales. Our goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice. We consider three broad categories of accelerators: Graphics Processing Units (GPUs), Field-Programmable Gate Arrays (FPGAs), and Application Specific Integrated Circuits (ASICs). These categories are comparatively studied to facilitate discussion of their relative trade-offs and to gain context for the current state of the art. We conclude by providing insights into the potential of emerging hardware platforms and algorithms for MD.