Serial replica exchange
Serial replica exchange
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DOI：
10.1021/jp064479e
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发表时间：
2007-02-15
影响因子：
3.3
通讯作者：
Berne, B. J.
中科院分区：
文献类型：
--
作者：
Hagen, Morten;Kim, Byungchan;Berne, B. J.
平行回火（或副本交换方法（REM））是一种强大的方法，用于加速具有粗糙能量景观的系统（如蛋白质）的构象状态采样，其中稳定的构象状态可以通过大的能量势垒分离。REM的通常实现是在本地计算机集群（或并行处理器）上执行的，其中不同的副本必须同步运行。在这里，我们提出了串行副本交换（SREM），一种方法，相当于标准的REM在效率方面异步运行在分布式网络的计算机。第二个优点是该方法极大地增强了容错能力，这使得在全球分布式计算环境（如Folding@Home）上研究生物系统成为可能。(1)为了证明概念，我们将SREM应用于明确水中的单个丙氨酸二肽分子。我们表明，SREM再现的REM确定的热力学和结构性质。
Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the sampling of conformational states of systems with rough energy landscapes, like proteins, where stable conformational states can be separated by large energy barriers. The usual implementation of the REM is performed on local computer clusters (or parallel processors) where the different replicas must be run synchronously. Here, we present serial replica exchange (SREM), a method that is equivalent to the standard REM in terms of efficiency yet runs asynchronously on a distributed network of computers. A second advantage is the method's greatly enhanced fault tolerance, which enables the study of biological systems on worldwide distributed computing environments, such as Folding@Home.(1) For proof of concept, we apply the SREM to a single alanine dipeptide molecule in explicit water. We show that the SREM reproduces the thermodynamic and structural properties determined by the REM.