Anton, a special-purpose machine for molecular dynamics simulation
Anton, a special-purpose machine for molecular dynamics simulation
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DOI：
10.1145/1364782.1364802
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发表时间：
2008-07-01
影响因子：
22.7
通讯作者：
Wang, Stanley C.
中科院分区：
文献类型：
--
作者：
Shaw, David E.;Deneroff, Martin M.;Wang, Stanley C.
执行涉及蛋白质和其他生物大分子的长时间、精确的分子动力学（MD）模拟的能力，原则上可以为生物学、化学和医学领域中一些最重要的当前悬而未决的问题提供答案。然而，一个广泛的生物有趣的现象，发生在毫秒级的时间尺度上-几个数量级超过目前最长的MD simulation.We描述了一个大规模的并行机称为安东，这应该是能够执行毫秒级经典MD模拟这样的生物分子系统。该机器计划于2008年底完成，基于512个相同的MD专用ASIC，使用专用高速通信网络以紧密耦合的方式进行交互。Anton设计用于使用新颖的并行算法和专用逻辑，以显著加速那些在典型MD模拟所需时间中占主导地位的计算。仿真算法的其余部分由每个芯片的可编程部分执行，该可编程部分实现了相当程度的并行性，同时保留了适应物理模型和仿真方法的预期进步所必需的灵活性。
The ability to perform long, accurate molecular dynamics ( MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond - several orders of magnitude beyond the duration of the longest current MD simulations.We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized highspeed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.