Characterization of Rare Events in Molecular Dynamics

Entropy

Carsten Hartmann¹  Ralf Banisch¹  Marco Sarich¹  Tomasz Badowski¹ 

[1] Institut für Mathematik, Freie Universit¨at Berlin, Arnimallee 6, 14195 Berlin, Germany; E-Mails:

关键词: rare events;    molecular dynamics;    optimal pathways;    stochastic control;    dynamic programming;    change of measure;    cumulant generating function;   

DOI  :  10.3390/e16010350

来源: mdpi

【 摘 要 】

A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski’s equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland