A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.
复制标题
DOI：
10.1021/ct0600464
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发表时间：
2006-01
影响因子：
5.5
通讯作者：
D. Zuckerman;E. Lyman
中科院分区：
文献类型：
--
作者：
D. Zuckerman;E. Lyman
复制品交换方法，也称为平行回火，在生物分子模拟中越来越受欢迎。我们问的方法是否可能是有效的固定温度的平衡采样的标准模拟方法相比。为了研究这个问题，我们做了一些简单的观察如何“快速”的高温分子模拟可以预期运行，以及如何表征效率的副本交换。虽然我们的结论仍然是完全建立，在文献中的一系列结果和我们自己的一些工作与50个原子的肽，我们是不乐观的复制品交换的生物分子的典型采样的效率。
The replica exchange approach, also called parallel tempering, is gaining popularity for biomolecular simulation. We ask whether the approach is likely to be efficient compared to standard simulation methods for fixed-temperature equilibrium sampling. To examine the issue, we make a number of straightforward observations on how "fast" high-temperature molecular simulations can be expected to run, as well as on how to characterize efficiency in replica exchange. Although our conclusions remain to be fully established, based on a range of results in the literature and some of our own work with a 50-atom peptide, we are not optimistic for the efficiency of replica exchange for canonical sampling of biomolecules.