利用副本交换模拟对生物分子的规范采样进行再审视。
A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.
作者信息
Zuckerman Daniel M, Lyman Edward
机构信息
Department of Computational Biology, School of Medicine, and Department of Environmental & Occupational Health, Graduate School of Public Health, Suite 3064 BST3, 3501 Fifth Avenue, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, ;
出版信息
J Chem Theory Comput. 2006;2(4):12001202. doi: 10.1021/ct0600464.
Abstract
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.
摘要
复制交换方法，也称为并行回火，在生物分子模拟中越来越受欢迎。我们探讨了与固定温度平衡采样的标准模拟方法相比，该方法是否可能高效。为了研究这个问题，我们对高温分子模拟预期运行的“速度”以及如何表征复制交换中的效率进行了一些直接观察。尽管我们的结论仍有待充分证实，但基于文献中的一系列结果以及我们自己对一个50原子肽的一些研究工作，我们对复制交换用于生物分子正则采样的效率并不乐观。
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本文引用的文献
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