Exchange Often and Properly in Replica Exchange Molecular Dynamics.
Exchange Often and Properly in Replica Exchange Molecular Dynamics.
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DOI：
10.1021/ct100281c
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发表时间：
2010-07
影响因子：
5.5
通讯作者：
Daniel J. Sindhikara;Daniel J. Emerson;A. Roitberg
中科院分区：
文献类型：
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作者：
Daniel J. Sindhikara;Daniel J. Emerson;A. Roitberg
我们之前的工作表明，在复制交换分子动力学中，应该非常频繁地尝试交换，从而提高效率并且不会产生不良影响。自那时以来，人们对这些主张是否可扩展到一般情况提出了一些问题。在这项工作中，我们以两种方式回答这个问题。首先，我们进行了一项研究，包括数千个原子的显式溶剂模拟测量交换尝试频率的影响。这表明，与前面的断言一致，高交换尝试频率允许最佳的探索构型空间的速率。其次，我们提出了一个解释的许多理论和技术陷阱时，实现副本交换，导致“不适当”的交流，导致错误的数据，加剧了高交换尝试频率。
Previous work by us showed that in replica exchange molecular dynamics, exchanges should be attempted extremely often, providing gains in efficiency and no undesired effects. Since that time some questions have been raised about the extendability of these claims to the general case. In this work, we answer this question in two ways. First, we perform a study measuring the effect of exchange attempt frequency in explicit solvent simulations including thousands of atoms. This shows, consistent with the previous assertion, that high exchange attempt frequency allows an optimal rate of exploration of configurational space. Second, we present an explanation of many theoretical and technical pitfalls when implementing replica exchange that cause "improper" exchanges resulting in erroneous data, exacerbated by high exchange attempt frequency.