A comparison of methods to compute the potential of mean force

被引：241

作者：

Trzesniak, Daniel ^{[1
]}

Kunz, Anna-Pitschna E. ^{[1
]}

van Gunsteren, Wilfred F. ^{[1
]}

机构：

[1] ETH, Phys Chem Lab, CH-8093 Zurich, Switzerland

来源：

CHEMPHYSCHEM | 2007年 / 8卷 / 01期

关键词：

computer chemistry; free-energy calculations; molecular dynamics; potential of mean force;

D O I：

10.1002/cphc.200600527

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：

Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is determined, this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane molecules in aqueous solution. We analyze all combinations of the type of sampling (unbiased umbrella-biased or constraint-biased), how to compute free energies (from density of states or force averaging) and the type of coordinate, system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.

引用

页码：162 / 169

页数：8

共 97 条

[1]

Allen M. P., 2009, Computer Simulation of Liquids

[2] MONTE-CARLO SIMULATIONS OF LIQUID NORMAL-BUTANE [J].