Literature DB >> 23004904

Improving the efficiency of extended ensemble simulations: the accelerated weight histogram method.

Jack Lidmar1.   

Abstract

We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a priori unknown weight parameters needed to produce flat histograms. The method combines several complementary techniques, namely, a Gibbs sampler for the parameter moves, a reweighting procedure to optimize data use, and a Bayesian update allowing for systematic refinement of the free energy estimate. In a certain limit the scheme reduces to the 1/t algorithm of B. E. Belardinelli and V. D. Pereyra [Phys. Rev. E 75, 046701 (2007)]. The performance of the method is studied on the two-dimensional Ising model, where comparison with the exact free energy is possible, and on an Ising spin glass.

Year:  2012        PMID: 23004904     DOI: 10.1103/PhysRevE.85.056708

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  4 in total

1.  Estimating thermodynamic expectations and free energies in expanded ensemble simulations: Systematic variance reduction through conditioning.

Authors:  Manuel Athènes; Pierre Terrier
Journal:  J Chem Phys       Date:  2017-05-21       Impact factor: 3.488

2.  Sequence dependency of canonical base pair opening in the DNA double helix.

Authors:  Viveca Lindahl; Alessandra Villa; Berk Hess
Journal:  PLoS Comput Biol       Date:  2017-04-03       Impact factor: 4.475

3.  Positive allosteric modulators of lecithin: Cholesterol acyltransferase adjust the orientation of the membrane-binding domain and alter its spatial free energy profile.

Authors:  Akseli Niemelä; Artturi Koivuniemi
Journal:  PLoS Comput Biol       Date:  2021-03-15       Impact factor: 4.475

4.  Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?

Authors:  Andreas H Larsen; Laura H John; Mark S P Sansom; Robin A Corey
Journal:  Biosci Rep       Date:  2022-04-29       Impact factor: 3.840

  4 in total

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