Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.
Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.
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DOI：
10.1021/acs.jpcb.6b02015
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发表时间：
2016-08-25
影响因子：
3.3
通讯作者：
Levy, Ronald M.
中科院分区：
文献类型：
--
作者：
Zhang, Bin W.;Dai, Wei;Gallicchio, Emilio;He, Peng;Xia, Junchao;Tan, Zhiqiang;Levy, Ronald M.
双交换分子动力学是一种多正则模拟技术，通常用于增强在崎岖的自由能景观上溶剂化生物分子的采样。虽然副本交换相对容易实现，但关于如何最有效地使用这种技术还有许多未回答的问题，特别是因为在实践中副本交换模拟经常不完全收敛。副本交换循环由一系列分子动力学步骤组成，所述一系列分子动力学步骤是在不同的哈密顿量下或在不同的热力学状态下移动的一组副本，随后是在不同的状态之间交换副本的一次或多次副本交换尝试。副本交换周期的构造方式影响系统平衡的速度。以主客体结合系统的长链分子动力学模拟为例，构建了一个Markov状态的副本交换模型（MSMRE），研究了不同的副本交换周期对采样效率的影响.我们分析了每个周期的副本交换尝试次数，每个周期的MD步骤数，以及两个参数之间的相互作用如何影响MSMRE模拟的最大隐含时间尺度。无限交换限制是副本交换中的一个重要概念。我们展示了如何估计无限交换限制从MSMRE“模拟的模拟”，以及从相对较短的运行的实际副本交换模拟的交换过渡矩阵的对角元素。
Replica exchange molecular dynamics is a multicanonical simulation technique commonly used to enhance the sampling of solvated biomolecules on rugged free energy landscapes. While replica exchange is relatively easy to implement, there are many unanswered questions about how to use this technique most effciently, especially because it is frequently the case in practice that replica exchange simulations are not fully converged. A replica exchange cycle consists of a series of molecular dynamics steps of a set of replicas moving under different Hamiltonians or at different thermodynamic states followed by one or more replica exchange attempts to swap replicas among the different states. How the replica exchange cycle is constructed affects how rapidly the system equilibrates. We have constructed a Markov state model of replica exchange (MSMRE) using long molecular dynamics simulations of a host–guest binding system as an example, in order to study how different implementations of the replica exchange cycle can affect the sampling effciency. We analyze how the number of replica exchange attempts per cycle, the number of MD steps per cycle, and the interaction between the two parameters affects the largest implied time scale of the MSMRE simulation. The infinite swapping limit is an important concept in replica exchange. We show how to estimate the infinite swapping limit from the diagonal elements of the exchange transition matrix constructed from MSMRE “simulations of simulations” as well as from relatively short runs of the actual replica exchange simulations.
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