Literature DB >> 18233891

Dynamics and optimal number of replicas in parallel tempering simulations.

Walter Nadler1, Ulrich H E Hansmann.   

Abstract

We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the control parameter discretization allow a treatment independent of the system in question. By analyzing mean first passage times across the control parameter space, we find an expression for the optimal number of replicas in simulations covering a given temperature range. Our results suggest a particular protocol to optimize the number of replicas in actual simulations.

Year:  2007        PMID: 18233891     DOI: 10.1103/PhysRevE.76.065701

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  8 in total

1.  Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine.

Authors:  Erbin He; Guanghui Yan; Jian Zhang; Jun Wang; Wenfei Li
Journal:  J Biol Phys       Date:  2016-01-12       Impact factor: 1.365

2.  Comparison of sampling efficiency between simulated tempering and replica exchange.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2008-10-07       Impact factor: 3.488

3.  Rapid equilibrium sampling initiated from nonequilibrium data.

Authors:  Xuhui Huang; Gregory R Bowman; Sergio Bacallado; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-29       Impact factor: 11.205

4.  Error and efficiency of replica exchange molecular dynamics simulations.

Authors:  Edina Rosta; Gerhard Hummer
Journal:  J Chem Phys       Date:  2009-10-28       Impact factor: 3.488

5.  Internal and environmental effects on folding and dimerization of the Alzheimer's β amyloid peptide.

Authors:  Priya Anand; Ulrich H E Hansmann
Journal:  Mol Simul       Date:  2011-05-01       Impact factor: 2.178

6.  Resolution exchange with tunneling for enhanced sampling of protein landscapes.

Authors:  Fatih Yasar; Alan J Ray; Ulrich H E Hansmann
Journal:  Phys Rev E       Date:  2022-07       Impact factor: 2.707

7.  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

8.  Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models.

Authors:  Ernesto Suárez; Joshua L Adelman; Daniel M Zuckerman
Journal:  J Chem Theory Comput       Date:  2016-07-11       Impact factor: 6.006

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.