Literature DB >> 15268578

The incomplete beta function law for parallel tempering sampling of classical canonical systems.

Cristian Predescu1, Mihaela Predescu, Cristian V Ciobanu.   

Abstract

We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the ratio of the temperatures. The law, called the incomplete beta function law, is valid in the limit that the two temperatures involved in swaps are close to one another. An empirical version of the law, which involves the heat capacity of the system, is developed and tested on a Lennard-Jones cluster. We argue that the best initial guess for the distribution of intermediate temperatures for parallel tempering is a geometric progression and we also propose a technique for the computation of optimal temperature schedules. Finally, we demonstrate that the swap efficiency of the parallel tempering method for condensed-phase systems decreases naturally to zero at least as fast as the inverse square root of the dimensionality of the physical system. Copyright 2004 American Institute of Physics

Year:  2004        PMID: 15268578     DOI: 10.1063/1.1644093

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  9 in total

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Authors:  Weihua Zheng; Michael Andrec; Emilio Gallicchio; Ronald M Levy
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4.  A generalized linear response framework for expanded ensemble and replica exchange simulations.

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Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

5.  Replica exchange statistical temperature Monte Carlo.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2009-03-28       Impact factor: 3.488

6.  On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods.

Authors:  Anthony Lee; Christopher Yau; Michael B Giles; Arnaud Doucet; Christopher C Holmes
Journal:  J Comput Graph Stat       Date:  2010-12-01       Impact factor: 2.302

7.  Evaluation of unrestrained replica-exchange simulations using dynamic walkers in temperature space for protein structure refinement.

Authors:  Mark A Olson; Michael S Lee
Journal:  PLoS One       Date:  2014-05-21       Impact factor: 3.240

8.  On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

Authors:  Mark A Olson
Journal:  Front Mol Biosci       Date:  2017-01-31

9.  Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation.

Authors:  Yannik Schälte; Jan Hasenauer
Journal:  Bioinformatics       Date:  2020-07-01       Impact factor: 6.937

  9 in total

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