Literature DB >> 19368436

Optimal replica exchange method combined with Tsallis weight sampling.

Jaegil Kim1, John E Straub.   

Abstract

A unified framework integrating the generalized ensemble sampling associated with the Tsallis weight [C. Tsallis, J. Stat. Phys. 52, 479 (1988)] and the replica exchange method (REM) has been proposed to accelerate the convergence of the conventional temperature REM (t-REM). Using the effective temperature formulation of the Tsallis weight sampling, it is shown that the average acceptance probability for configurational swaps between neighboring replicas in the combination of Tsallis weight sampling and REM (Tsallis-REM) is directly proportional to an overlap integral of the energy distributions of neighboring replicas as in the t-REM. Based on this observation, we suggest a robust method to select optimal Tsallis parameters in the conventional parametrization scheme and present new parametrization schemes for the Tsallis-REM, which significantly improves the acceptance of configurational swaps by systematically modulating energy overlaps between neighboring replicas. The distinguished feature of our method is that all relevant parameters in the Tsallis-REM are automatically determined from the equilibrium phase simulation using the t-REM. The overall performance of our method is explicitly demonstrated for various simulation conditions for the Lennard-Jones 31 atom clusters, exhibiting a double-funneled energy landscape.

Mesh:

Year:  2009        PMID: 19368436      PMCID: PMC2736612          DOI: 10.1063/1.3108523

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


  43 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.  Tsallis dynamics using the Nosé-Hoover approach.

Authors:  Ikuo Fukuda; Haruki Nakamura
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-01-09

3.  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

4.  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

5.  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

6.  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

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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  4 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.  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

4.  Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.

Authors:  Anuradha Mittal; Nicholas Lyle; Tyler S Harmon; Rohit V Pappu
Journal:  J Chem Theory Comput       Date:  2014-06-03       Impact factor: 6.006

  4 in total

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