Literature DB >> 19334813

Replica exchange statistical temperature Monte Carlo.

Jaegil Kim1, Thomas Keyes, John E Straub.   

Abstract

The replica exchange statistical temperature Monte Carlo algorithm (RESTMC) is presented, extending the single-replica STMC algorithm [J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601 (2006)] to alleviate the slow convergence of the conventional temperature replica exchange method (t-REM) with increasing system size. In contrast to the Gibbs-Boltzmann sampling at a specific temperature characteristic of the standard t-REM, RESTMC samples a range of temperatures in each replica and achieves a flat energy sampling employing the generalized sampling weight, which is automatically determined via the dynamic modification of the replica-dependent statistical temperature. Faster weight determination, through the dynamic update of the statistical temperature, and the flat energy sampling, maximizing energy overlaps between neighboring replicas, lead to a considerable acceleration in the convergence of simulations even while employing significantly fewer replicas. The performance of RESTMC is demonstrated and quantitatively compared with that of the conventional t-REM under varying simulation conditions for Lennard-Jones 19, 31, and 55 atomic clusters, exhibiting single- and double-funneled energy landscapes.

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Year:  2009        PMID: 19334813      PMCID: PMC2736574          DOI: 10.1063/1.3095422

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


  44 in total

1.  Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram.

Authors:  F Wang; D P Landau
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-10-17

2.  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

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

Authors:  Cristian Predescu; Mihaela Predescu; Cristian V Ciobanu
Journal:  J Chem Phys       Date:  2004-03-01       Impact factor: 3.488

4.  Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights.

Authors:  Jae Gil Kim; Yoshifumi Fukunishi; Akinori Kidera; Haruki Nakamura
Journal:  J Chem Phys       Date:  2004-09-22       Impact factor: 3.488

5.  Multiple structural transformations in Lennard-Jones clusters: generic versus size-specific behavior.

Authors:  Vladimir A Mandelshtam; Pavel A Frantsuzov
Journal:  J Chem Phys       Date:  2006-05-28       Impact factor: 3.488

6.  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

7.  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

8.  Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: inherent structure analysis and statistical temperature molecular dynamics simulation.

Authors:  Jaegil Kim; Thomas Keyes
Journal:  J Phys Chem B       Date:  2007-12-19       Impact factor: 2.991

9.  Resolution exchange simulation.

Authors:  Edward Lyman; F Marty Ytreberg; Daniel M Zuckerman
Journal:  Phys Rev Lett       Date:  2006-01-18       Impact factor: 9.161

Review 10.  Novel methods of sampling phase space in the simulation of biological systems.

Authors:  B J Berne; J E Straub
Journal:  Curr Opin Struct Biol       Date:  1997-04       Impact factor: 6.809

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  7 in total

1.  Generalized replica exchange method.

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

2.  Generalized simulated tempering for exploring strong phase transitions.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

3.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

Authors:  Hernán Stamati; Cecilia Clementi; Lydia E Kavraki
Journal:  Proteins       Date:  2010-02-01

4.  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

5.  Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods.

Authors:  Lili Gai; Thomas Vogel; Katie A Maerzke; Christopher R Iacovella; David P Landau; Peter T Cummings; Clare McCabe
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

6.  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

7.  Anatomic features, tolerance index, secondary metabolites and protein content of chickpea (Cicer arietinum) seedlings under cadmium induction and identification of PCS and FC genes.

Authors:  Elham Mohajel Kazemi; Maryam Kolahi; Milad Yazdi; Andrea Goldson-Barnaby
Journal:  Physiol Mol Biol Plants       Date:  2020-07-29
  7 in total

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