Markov models of molecular kinetics: Generation and validation
Markov models of molecular kinetics: Generation and validation
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DOI：
10.1063/1.3565032
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发表时间：
2011-05-07
影响因子：
4.4
通讯作者：
Noe, Frank
中科院分区：
文献类型：
--
作者：
Prinz, Jan-Hendrik;Wu, Hao;Noe, Frank
分子动力学的马尔可夫状态模型（MSMs）近年来得到了广泛的应用，其中分子的长期统计动力学是由一个离散分割的构型空间上的马尔可夫链来近似的。与直接的分子动力学模拟和分析相比，这种方法有许多吸引人的特点，包括通过从短轨迹中提取长时间动力学信息来减轻采样问题的潜力，以及直接计算各种静态和动态分子观测值的期望值和统计不确定性的能力。本文总结了msm的生成和验证的最新进展，并给出了一些重要的新结果。我们描述了用MSM模拟分子动力学所产生的近似误差的上界，我们表明，这个误差可以用惊人的小的努力使任意小。与以往的实践相比，很明显，最佳的MSM不是通过最亚稳态离散得到的，但如果在过渡态附近引入非亚稳态，则MSM可以得到很大的改善。此外，我们还表明，没有必要通过状态空间划分来解决所有的慢过程，但是单个感兴趣的动态过程可以单独解决。我们还提出了一个可逆转移矩阵的有效估计器和一个鲁棒测试，以验证MSM再现分子动力学数据的动力学。(C) 2011年美国物理研究所。(doi: 10.1063/1.3565032)
Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data. (C) 2011 American Institute of Physics. [doi:10.1063/1.3565032]