Literature DB >> 20095723

Error and efficiency of simulated tempering simulations.

Edina Rosta1, Gerhard Hummer.   

Abstract

We derive simple analytical expressions for the error and computational efficiency of simulated tempering (ST) simulations. The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. An extension to the multistate case is described. We show that the relative gain in efficiency of ST simulations over regular molecular dynamics (MD) or Monte Carlo (MC) simulations is given by the ratio of their reactive fluxes, i.e., the number of transitions between the two states summed over all ST temperatures divided by the number of transitions at the single temperature of the MD or MC simulation. This relation for the efficiency is derived for the limit in which changes in the ST temperature are fast compared to the two-state transitions. In this limit, ST is most efficient. Our expression for the maximum efficiency gain of ST simulations is essentially identical to the corresponding expression derived by us for replica exchange MD and MC simulations [E. Rosta and G. Hummer, J. Chem. Phys. 131, 165102 (2009)] on a different route. We find quantitative agreement between predicted and observed efficiency gains in a test against ST and replica exchange MC simulations of a two-dimensional Ising model. Based on the efficiency formula, we provide recommendations for the optimal choice of ST simulation parameters, in particular, the range and number of temperatures, and the frequency of attempted temperature changes.

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Year:  2010        PMID: 20095723      PMCID: PMC2821152          DOI: 10.1063/1.3290767

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


  17 in total

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4.  Exchange frequency in replica exchange molecular dynamics.

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Journal:  J Chem Phys       Date:  2008-01-14       Impact factor: 3.488

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

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Journal:  J Chem Phys       Date:  2008-10-07       Impact factor: 3.488

6.  Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

Authors:  Xuhui Huang; Gregory R Bowman; Vijay S Pande
Journal:  J Chem Phys       Date:  2008-05-28       Impact factor: 3.488

7.  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

8.  Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1996-11

9.  Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.

Authors:  Xavier Periole; Alan E Mark
Journal:  J Chem Phys       Date:  2007-01-07       Impact factor: 3.488

10.  Thermostat artifacts in replica exchange molecular dynamics simulations.

Authors:  Edina Rosta; Nicolae-Viorel Buchete; Gerhard Hummer
Journal:  J Chem Theory Comput       Date:  2009       Impact factor: 6.006

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  6 in total

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Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

2.  Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

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Journal:  J Chem Phys       Date:  2016-01-21       Impact factor: 3.488

3.  Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

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Journal:  Chem Soc Rev       Date:  2014-04-23       Impact factor: 54.564

Review 6.  Enhanced sampling without borders: on global biasing functions and how to reweight them.

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  6 in total

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