Literature DB >> 16468860

A general framework for non-Boltzmann Monte Carlo sampling.

Charlles R A Abreu1, Fernando A Escobedo.   

Abstract

Non-Boltzmann sampling (NBS) methods have been extensively employed in recent years, mainly due to their ability to enhance ergodicity in simulations of complex systems. In addition, they make possible reliable computation of equilibrium properties (ensemble averages, free-energy differences, and potentials of mean force) over continuous ranges of thermodynamic conditions. In this work, we put forward a general and systematic framework for NBS methods that allows a single set of equations and procedures to be applied to diverse systems. Moreover, we show how to exploit simulation data most effectively by obtaining continuous profiles of any mechanical properties, including structural quantities not directly related to the ensemble parameters. Finally, we demonstrate the usefulness of the developed formulation by applying it to spin systems, Lennard-Jones fluids, and a model protein molecule (both in isolation and in the proximity of a flat wall).

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Year:  2006        PMID: 16468860     DOI: 10.1063/1.2165188

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


  4 in total

1.  Re-entrant melting as a design principle for DNA-coated colloids.

Authors:  Stefano Angioletti-Uberti; Bortolo M Mognetti; Daan Frenkel
Journal:  Nat Mater       Date:  2012-04-29       Impact factor: 43.841

2.  A black-box re-weighting analysis can correct flawed simulation data.

Authors:  F Marty Ytreberg; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2008-06-10       Impact factor: 11.205

3.  Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics.

Authors:  Feng Wang; Steven J Stuart; Robert A Latour
Journal:  Biointerphases       Date:  2008       Impact factor: 2.456

Review 4.  Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.

Authors:  Hagai Meirovitch; Srinath Cheluvaraja; Ronald P White
Journal:  Curr Protein Pept Sci       Date:  2009-06       Impact factor: 3.272

  4 in total

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