Literature DB >> 23205986

Rare-event sampling: occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods.

J D Doll1, Nuria Plattner, David L Freeman, Yufei Liu, Paul Dupuis.   

Abstract

In the present paper we identify a rigorous property of a number of tempering-based Monte Carlo sampling methods, including parallel tempering as well as partial and infinite swapping. Based on this property we develop a variety of performance measures for such rare-event sampling methods that are broadly applicable, informative, and straightforward to implement. We illustrate the use of these performance measures with a series of applications involving the equilibrium properties of simple Lennard-Jones clusters, applications for which the performance levels of partial and infinite swapping approaches are found to be higher than those of conventional parallel tempering.

Year:  2012        PMID: 23205986     DOI: 10.1063/1.4765060

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


  3 in total

Review 1.  Multiscale implementation of infinite-swap replica exchange molecular dynamics.

Authors:  Tang-Qing Yu; Jianfeng Lu; Cameron F Abrams; Eric Vanden-Eijnden
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-03       Impact factor: 11.205

2.  Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.

Authors:  Brajesh Narayan; Colm Herbert; Ye Yuan; Brian J Rodriguez; Bernard R Brooks; Nicolae-Viorel Buchete
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

3.  Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations.

Authors:  Andrew J Ballard; David J Wales
Journal:  J Chem Theory Comput       Date:  2014-11-04       Impact factor: 6.006

  3 in total

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