Coarse master equation from Bayesian analysis of replica molecular dynamics simulations
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations
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DOI：
10.1021/jp046448u
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发表时间：
2005-04-14
影响因子：
3.3
通讯作者：
Hummer, G
中科院分区：
文献类型：
--
作者：
Sriraman, S;Kevrekidis, LG;Hummer, G
我们用贝叶斯推理从分子动力学模拟中推导出一个粗主方程的速率系数。利用多个短仿真轨迹的结果来估计传播量。作为传播因子的乘积构造的似然函数提供了决定马尔可夫主方程的速率矩阵中自由系数的后验分布。利用轨迹“路径”作为观测，讨论了非马尔可夫动力学的扩展。用马尔可夫方法描述了溶解在水中的短碳纳米管的填充和清空跃迁。我们证明了精确的热力学和动力学性质，如自由能面和动力学速率系数，可以从通过贝叶斯推理得到的粗略主方程中计算出来。
We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.