重新审视平均力势与自由能分布之间的确切关系。

Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile.

作者信息

den Otter Wouter K

机构信息

Multi Scale Mechanics, Faculty of Engineering Technology, and Computational BioPhysics, Faculty of Science and Technology, and MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands.

出版信息

J Chem Theory Comput. 2013 Sep 10;9(9):3861-5. doi: 10.1021/ct400134d. Epub 2013 Aug 26.

DOI:10.1021/ct400134d

PMID:26592381

Abstract

Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York [J. Chem. Theory Comput. 2012, 8, 3998-4003] suggest replacing Fixman's mass-metric correction with its inverse and adding a Jacobian contribution to the potential of mean constraint force. This letter refutes both suggestions, discusses the underlying interpretation problems, and provides supporting numerical simulations.

摘要

在通过分子动力学模拟计算自由能分布时，约束条件很方便，但它们会微妙地改变相空间分布。在本期刊最近一篇相关标题的信函中，Wong和York [《化学理论与计算杂志》2012年，8卷，3998 - 4003页] 建议用Fixman质量度量校正的倒数来代替它，并在平均约束势力的势能中加入雅可比行列式贡献。本信函反驳了这两个建议，讨论了潜在的解释问题，并提供了支持性的数值模拟。