Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning
Optimization of Umbrella Sampling Replica Exchange Molecular Dynamics by Replica Positioning
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DOI：
10.1021/ct400366h
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发表时间：
2013-11-01
影响因子：
5.5
通讯作者：
Roitberg, Adrian E.
中科院分区：
文献类型：
--
作者：
Dashti, Danial Sabri;Roitberg, Adrian E.
在伞形抽样模拟中，抽样窗口的位置对收敛速度和计算效率有影响。当这样的模拟是再加上一个哈密尔顿副本交换设置，我们表明，这样的定位可以优化的结果的最大收敛。本文提出了一种在伞形取样复制交换（USRE）分子动力学（MD）中估算反应坐标上任意两个位置间交换接受比（EJ）的方法。我们设计了一个评分函数来优化副本集（窗口）的位置。通过最大化评分函数，我们使所有的邻居副本对的平均值相同，提高了方法的效率。我们测试了我们的算法，通过采样扭转丁烷在隐式溶剂和研究盐桥在显式溶剂。我们发现，优化的副本集恢复正确的自由能分布比等距伞快得多。
The positioning of sampling windows in an umbrella sampling simulation has an effect on the rate of convergence and computational efficiency. When such simulation is coupled with a Hamiltonian replica exchange setup, we show that such positioning can be optimized for maximal convergence of the results. We present a method for estimating the exchange acceptance ratio (EAR) between two arbitrary positions on a reaction coordinate in umbrella sampling replica exchange (USRE) molecular dynamics (MD). We designed a scoring function to optimize the position of the set of replicas (windows). By maximizing the scoring function, we make EAR the same for all neighbor replica pairs, increasing the efficiency of the method. We tested our algorithm by sampling a torsion for butane in implicit solvent and by studying a salt bridge in explicit solvent. We found that the optimized set of replicas recovers the correct free energy profile much faster than for equally spaced umbrellas.