Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.
Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.
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DOI：
10.1021/ct401065r
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发表时间：
2014-07-08
影响因子：
5.5
通讯作者：
Zuckerman, Daniel M.
中科院分区：
文献类型：
--
作者：
Suarez, Ernesto;Lettieri, Steven;Zwier, Matthew C.;Stringer, Carsen A.;Subramanian, Sundar Raman;Chong, Lillian T.;Zuckerman, Daniel M.
平衡形式上可以表示为一个非耦合系统的合奏经历无偏动力学，其中详细的平衡保持。许多非平衡过程可以用平衡系综的适当子集来描述。这里，我们采用“加权系综”（WE）模拟协议[Huber和Kim，Biophys. J.1996，70，97-110]来生成平衡轨迹集合并提取用于计算动力学量的非平衡子集。不需要提前选择国家。该程序正式允许估计任意状态之间的动力学速率选择后的模拟，沿着与他们的平衡人口。我们还描述了一个相关的历史相关的矩阵估计的平衡和非平衡可观的相空间时，已被划分为任意的非马尔可夫区域，无论是在我们还是普通的模拟程序。在这个原理验证的研究中，这些方法成功地应用和验证两个分子系统：明确的溶剂化甲烷协会和隐含的溶剂化Ala 4肽。我们对WE计算中仍然存在的挑战进行评论。
Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the “weighted ensemble” (WE) simulation protocol [Huber and Kim, Biophys. J.1996, 70, 97–110] to generate equilibrium trajectory ensembles and extract nonequilibrium subsets for computing kinetic quantities. States do not need to be chosen in advance. The procedure formally allows estimation of kinetic rates between arbitrary states chosen after the simulation, along with their equilibrium populations. We also describe a related history-dependent matrix procedure for estimating equilibrium and nonequilibrium observables when phase space has been divided into arbitrary non-Markovian regions, whether in WE or ordinary simulation. In this proof-of-principle study, these methods are successfully applied and validated on two molecular systems: explicitly solvated methane association and the implicitly solvated Ala4 peptide. We comment on challenges remaining in WE calculations.
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