Error analysis and efficient sampling in Markovian state models for molecular dynamics

被引:138
作者
Singhal, N
Pande, VS [1 ]
机构
[1] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
D O I
10.1063/1.2116947
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
In previous work, we described a Markovian state model (MSM) for analyzing molecular-dynamics trajectories, which involved grouping conformations into states and estimating the transition probabilities between states. In this paper, we analyze the errors in this model caused by finite sampling. We give different methods with various approximations to determine the precision of the reported mean first passage times. These approximations are validated on an 87 state toy Markovian system. In addition, we propose an efficient and practical sampling algorithm that uses these error calculations to build a MSM that has the same precision in mean first passage time values but requires an order of magnitude fewer samples. We also show how these methods can be scaled to large systems using sparse matrix methods.
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页数:13
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