Literature DB >> 16606249

Equilibrium free energies from nonequilibrium metadynamics.

Giovanni Bussi1, Alessandro Laio, Michele Parrinello.   

Abstract

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.

Entities:  

Year:  2006        PMID: 16606249     DOI: 10.1103/PhysRevLett.96.090601

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  65 in total

1.  Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations.

Authors:  Meher K Prakash; Alessandro Barducci; Michele Parrinello
Journal:  Biophys J       Date:  2010-07-21       Impact factor: 4.033

2.  The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections.

Authors:  Volodymyr Babin; Christopher Roland; Thomas A Darden; Celeste Sagui
Journal:  J Chem Phys       Date:  2006-11-28       Impact factor: 3.488

3.  Nucleotide-dependent conformational states of actin.

Authors:  Jim Pfaendtner; Davide Branduardi; Michele Parrinello; Thomas D Pollard; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-20       Impact factor: 11.205

4.  Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations.

Authors:  Han Zheng; Yingkai Zhang
Journal:  J Chem Phys       Date:  2008-05-28       Impact factor: 3.488

5.  Introducing sampling entropy in repository based adaptive umbrella sampling.

Authors:  Han Zheng; Yingkai Zhang
Journal:  J Chem Phys       Date:  2009-12-07       Impact factor: 3.488

6.  Implementation of Accelerated Molecular Dynamics in NAMD.

Authors:  Yi Wang; Christopher B Harrison; Klaus Schulten; J Andrew McCammon
Journal:  Comput Sci Discov       Date:  2011

7.  Molecular motions in drug design: the coming age of the metadynamics method.

Authors:  Xevi Biarnés; Salvatore Bongarzone; Attilio Vittorio Vargiu; Paolo Carloni; Paolo Ruggerone
Journal:  J Comput Aided Mol Des       Date:  2011-02-17       Impact factor: 3.686

8.  Adaptive conformational sampling based on replicas.

Authors:  Jeremy Curuksu
Journal:  J Math Biol       Date:  2011-06-08       Impact factor: 2.259

9.  Insight into the folding inhibition of the HIV-1 protease by a small peptide.

Authors:  Massimiliano Bonomi; Francesco L Gervasio; Guido Tiana; Davide Provasi; Ricardo A Broglia; Michele Parrinello
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

10.  Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

Authors:  Claudio Melis; Giovanni Bussi; Sarah C R Lummis; Carla Molteni
Journal:  J Phys Chem B       Date:  2009-09-03       Impact factor: 2.991

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