Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics

被引：271

作者：

Bonomi, M. ^{[1
]}

Barducci, A. ^{[1
]}

Parrinello, M. ^{[1
]}

机构：

[1] Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2009年 / 30卷 / 11期

关键词：

molecular dynamics; metadynamics; Boltzmann distribution; reweighting; umbrella sampling; MOLECULAR-DYNAMICS SIMULATION; FREE-ENERGY CALCULATIONS; CONFORMATIONAL TRANSITIONS; PHASE-TRANSITIONS; RATE CONSTANTS; BETA-HAIRPIN; MEAN FORCE; PROTEIN; SYSTEMS; ALGORITHM;

D O I：

10.1002/jcc.21305

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 1615-1621, 2009

引用

页码：1615 / 1621

页数：7

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