通过离散弛豫路径采样进行马尔可夫状态建模和动力学粗粒化
Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.
作者信息
Fačkovec B, Vanden-Eijnden E, Wales D J
机构信息
Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.
Courant Institute, New York University, 251 Mercer Street, New York, New York 10012, USA.
出版信息
J Chem Phys. 2015 Jul 28;143(4):044119. doi: 10.1063/1.4926940.
A method is derived to coarse-grain the dynamics of complex molecular systems to a Markov jump process (MJP) describing how the system jumps between cells that fully partition its state space. The main inputs are relaxation times for each pair of cells, which are shown to be robust with respect to positioning of the cell boundaries. These relaxation times can be calculated via molecular dynamics simulations performed in each cell separately and are used in an efficient estimator for the rate matrix of the MJP. The method is illustrated through applications to Sinai billiards and a cluster of Lennard-Jones discs.
一种方法被推导出来，用于将复杂分子系统的动力学粗粒化为一个马尔可夫跳跃过程（MJP），该过程描述了系统如何在完全划分其状态空间的单元格之间跳跃。主要输入是每对单元格的弛豫时间，结果表明这些弛豫时间对于单元格边界的定位具有鲁棒性。这些弛豫时间可以通过在每个单元格中分别进行的分子动力学模拟来计算，并用于MJP速率矩阵的有效估计器中。通过对 Sinai 台球和 Lennard-Jones 圆盘簇的应用来说明该方法。
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