Exact milestoning
Exact milestoning
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DOI：
10.1063/1.4913399
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发表时间：
2015-03-07
影响因子：
4.4
通讯作者：
Elber, Ron
中科院分区：
文献类型：
--
作者：
Bello-Rivas, Juan M.;Elber, Ron
本文介绍了一种计算粒子系统动力学和热力学性质的新理论和精确的计算机算法。该算法避免陷入亚稳态，这是典型的挑战分子动力学（MD）模拟粗糙的能量景观。它基于将整个空间划分为Voronoi单元。先验知识或空间点的粗采样提供了Voronoi单元的中心。短时间的轨迹计算之间的边界的细胞，我们称之为里程碑，并用于确定通量的里程碑。通量函数是新理论的一个重要组成部分，它在里程碑的分辨率上提供了系统统计力学的完整描述。我们说明了精确的里程碑方法的准确性和效率，通过比较使用精确的里程碑长轨迹的结果和相应的福克-普朗克方程的解决方案的模型系统上获得的数值结果。该理论使用的方程类似于2004年引入的近似里程碑方法[A. K. Faradjian和R. Elber，J.Chem.Phys.120（23），10880-10889（2004）]。然而，目前的配方是准确的，仍然是显着更有效的比简单的MD模拟系统的研究。(c)2015 AIP Publishing LLC.
A new theory and an exact computer algorithm for calculating kinetics and thermodynamic properties of a particle system are described. The algorithm avoids trapping in metastable states, which are typical challenges for Molecular Dynamics (MD) simulations on rough energy landscapes. It is based on the division of the full space into Voronoi cells. Prior knowledge or coarse sampling of space points provides the centers of the Voronoi cells. Short time trajectories are computed between the boundaries of the cells that we call milestones and are used to determine fluxes at the milestones. The flux function, an essential component of the new theory, provides a complete description of the statistical mechanics of the system at the resolution of the milestones. We illustrate the accuracy and efficiency of the exact Milestoning approach by comparing numerical results obtained on a model system using exact Milestoning with the results of long trajectories and with a solution of the corresponding Fokker-Planck equation. The theory uses an equation that resembles the approximate Milestoning method that was introduced in 2004 [A. K. Faradjian and R. Elber, J. Chem. Phys. 120(23), 10880-10889 (2004)]. However, the current formulation is exact and is still significantly more efficient than straightforward MD simulations on the system studied. (c) 2015 AIP Publishing LLC.