Equilibrium free energies from nonequilibrium metadynamics

被引:340
作者
Bussi, G [1 ]
Laio, A [1 ]
Parrinello, M [1 ]
机构
[1] Eidgenossische Tech Hochsch Zurich, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland
关键词
D O I
10.1103/PhysRevLett.96.090601
中图分类号
O4 [物理学];
学科分类号
0702 ;
摘要
In this Letter we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to model Langevin dynamics and determine the equilibrium distribution of a collection of simulations. We demonstrate that the reconstructed free energy is an unbiased estimate of the underlying free energy and analytically derive an expression for the error. The present results can be applied to other history-dependent stochastic processes, such as Wang-Landau sampling.
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页数:4
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共 26 条
[1]   Exploring intramolecular reactions in complex systems with metadynamics: The case of the malonate anions [J].
Asciutto, E ;
Sagui, C .
JOURNAL OF PHYSICAL CHEMISTRY A, 2005, 109 (34) :7682-7687
[2]   Calculating free energies using average force [J].
Darve, E ;
Pohorille, A .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (20) :9169-9183
[3]   Perspective on the reactions between F- and CH3CH2F:: The free energy landscape of the E2 and SN2 reaction channels [J].
Ensing, B ;
Klein, ML .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (19) :6755-6759
[4]   'Coarse' integration/bifurcation analysis via microscopic simulators: micro-Galerkin methods [J].
Gear, CW ;
Kevrekidis, IG ;
Theodoropoulos, C .
COMPUTERS & CHEMICAL ENGINEERING, 2002, 26 (7-8) :941-963
[5]   Equilibrium time correlation functions from irreversible transformations in trajectory space [J].
Geissler, PL ;
Dellago, C .
JOURNAL OF PHYSICAL CHEMISTRY B, 2004, 108 (21) :6667-6672
[6]   Flexible docking in solution using metadynamics [J].
Gervasio, FL ;
Laio, A ;
Parrinello, M .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2005, 127 (08) :2600-2607
[7]   Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force [J].
Grubmuller, H ;
Heymann, B ;
Tavan, P .
SCIENCE, 1996, 271 (5251) :997-999
[8]   LOCAL ELEVATION - A METHOD FOR IMPROVING THE SEARCHING PROPERTIES OF MOLECULAR-DYNAMICS SIMULATION [J].
HUBER, T ;
TORDA, AE ;
VANGUNSTEREN, WF .
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, 8 (06) :695-708
[9]   Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations [J].
Hummer, G ;
Kevrekidis, IG .
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (23) :10762-10773
[10]   Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics [J].
Iannuzzi, M ;
Laio, A ;
Parrinello, M .
PHYSICAL REVIEW LETTERS, 2003, 90 (23) :4