Literature DB >> 22025687

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Jerome P Nilmeier1, Gavin E Crooks, David D L Minh, John D Chodera.   

Abstract

Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Here, we introduce a new class of moves based on nonequilibrium dynamics: Candidate configurations are generated through a finite-time process in which a system is actively driven out of equilibrium, and accepted with criteria that preserve the equilibrium distribution. The acceptance rule is similar to the Metropolis acceptance probability, but related to the nonequilibrium work rather than the instantaneous energy difference. Our method is applicable to sampling from both a single thermodynamic state or a mixture of thermodynamic states, and allows both coordinates and thermodynamic parameters to be driven in nonequilibrium proposals. Whereas generating finite-time switching trajectories incurs an additional cost, driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times. Using nonequilibrium driven processes vastly expands the repertoire of useful Monte Carlo proposals in simulations of dense solvated systems.

Mesh:

Year:  2011        PMID: 22025687      PMCID: PMC3215031          DOI: 10.1073/pnas.1106094108

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  37 in total

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Authors:  M Athènes
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-10-28

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Journal:  Phys Rev Lett       Date:  1989-01-23       Impact factor: 9.161

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Authors:  Robert B Best; Gerhard Hummer
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5.  Optimal finite-time processes in stochastic thermodynamics.

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Journal:  Phys Rev Lett       Date:  2007-03-07       Impact factor: 9.161

6.  Equilibrium free energies from fast-switching trajectories with large time steps.

Authors:  Wolfgang Lechner; Harald Oberhofer; Christoph Dellago; Phillip L Geissler
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

7.  Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

Authors:  Bernd Ensing; Marco De Vivo; Zhiwei Liu; Preston Moore; Michael L Klein
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8.  Molecular simulation with variable protonation states at constant pH.

Authors:  Harry A Stern
Journal:  J Chem Phys       Date:  2007-04-28       Impact factor: 3.488

9.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

10.  Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages.

Authors:  David D L Minh; John D Chodera
Journal:  J Chem Phys       Date:  2009-10-07       Impact factor: 3.488

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  26 in total

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Authors:  Mathias Ferber; Jan Kosinski; Alessandro Ori; Umar J Rashid; María Moreno-Morcillo; Bernd Simon; Guillaume Bouvier; Paulo Ricardo Batista; Christoph W Müller; Martin Beck; Michael Nilges
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Authors:  Jeremy Copperman; David Aristoff; Dmitrii E Makarov; Gideon Simpson; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2019-11-07       Impact factor: 3.488

9.  A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.

Authors:  Tai-Sung Lee; Brian K Radak; Anna Pabis; Darrin M York
Journal:  J Chem Theory Comput       Date:  2012-12-12       Impact factor: 6.006

10.  Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Authors:  Brian K Radak; Christophe Chipot; Donghyuk Suh; Sunhwan Jo; Wei Jiang; James C Phillips; Klaus Schulten; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2017-11-22       Impact factor: 6.006

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