Literature DB >> 19592512

Replica exchange with nonequilibrium switches.

Andrew J Ballard1, Christopher Jarzynski.   

Abstract

We introduce a replica exchange (parallel tempering) method in which attempted configuration swaps are generated using nonequilibrium work simulations. By effectively increasing phase space overlap, this approach mitigates the need for many replicas. We illustrate our method by using a model system and show that it is able to achieve the computational efficiency of ordinary replica exchange, using fewer replicas.

Mesh：

Year:  2009        PMID： 19592512      PMCID： PMC2718341          DOI： 10.1073/pnas.0900406106

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


  22 in total

1.  Replica-exchange method using the generalized effective potential.

Authors:  Soonmin Jang; Seokmin Shin; Youngshang Pak
Journal:  Phys Rev Lett       Date:  2003-08-01       Impact factor: 9.161

2.  Replica Monte Carlo simulation of spin glasses.

Authors: 
Journal:  Phys Rev Lett       Date:  1986-11-24       Impact factor: 9.161

3.  Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?

Authors:  Harald Oberhofer; Christoph Dellago; Phillip L Geissler
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

4.  Optimized parallel tempering simulations of proteins.

Authors:  Simon Trebst; Matthias Troyer; Ulrich H E Hansmann
Journal:  J Chem Phys       Date:  2006-05-07       Impact factor: 3.488

5.  Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent.

Authors:  Pu Liu; Xuhui Huang; Ruhong Zhou; B J Berne
Journal:  J Phys Chem B       Date:  2006-09-28       Impact factor: 2.991

6.  Simulating replica exchange simulations of protein folding with a kinetic network model.

Authors:  Weihua Zheng; Michael Andrec; Emilio Gallicchio; Ronald M Levy
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-18       Impact factor: 11.205

7.  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

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.  Exchange frequency in replica exchange molecular dynamics.

Authors:  Daniel Sindhikara; Yilin Meng; Adrian E Roitberg
Journal:  J Chem Phys       Date:  2008-01-14       Impact factor: 3.488

Review 10.  Parallel tempering: theory, applications, and new perspectives.

Authors:  David J Earl; Michael W Deem
Journal:  Phys Chem Chem Phys       Date:  2005-12-07       Impact factor: 3.676
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  14 in total

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

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

2.  Generalized replica exchange method.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2010-06-14       Impact factor: 3.488

3.  Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

Authors:  Yunjie Chen; Seyit Kale; Jonathan Weare; Aaron R Dinner; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2016-03-25       Impact factor: 6.006

4.  Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail.

Authors:  Carsten Kutzner; Helmut Grubmüller; Bert L de Groot; Ulrich Zachariae
Journal:  Biophys J       Date:  2011-08-17       Impact factor: 4.033

5.  Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Authors:  Xiongwu Wu; Milan Hodoscek; Bernard R Brooks
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

Review 6.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

7.  From data to noise to data for mixing physics across temperatures with generative artificial intelligence.

Authors:  Yihang Wang; Lukas Herron; Pratyush Tiwary
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-04       Impact factor: 12.779

8.  Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.

Authors:  Mahmoud Moradi; Emad Tajkhorshid
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-04       Impact factor: 11.205

9.  Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

Authors:  Bin W Zhang; Wei Dai; Emilio Gallicchio; Peng He; Junchao Xia; Zhiqiang Tan; Ronald M Levy
Journal:  J Phys Chem B       Date:  2016-04-29       Impact factor: 2.991

10.  Equilibrium molecular thermodynamics from Kirkwood sampling.

Authors:  Sandeep Somani; Yuko Okamoto; Andrew J Ballard; David J Wales
Journal:  J Phys Chem B       Date:  2015-05-12       Impact factor: 2.991
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