Literature DB >> 17994804

Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems.

Fernando A Escobedo1.   

Abstract

In the Grand Canonical, osmotic, and Gibbs ensembles, chemical potential equilibrium is attained via transfers of molecules between the system and either a reservoir or another subsystem. In this work, the expanded ensemble (EXE) methods described in part I [F. A. Escobedo and F. J. Martinez-Veracoechea, J. Chem. Phys. 127, 174103 (2007)] of this series are extended to these ensembles to overcome the difficulties associated with implementing such whole-molecule transfers. In EXE, such moves occur via a target molecule that undergoes transitions through a number of intermediate coupling states. To minimize the tunneling time between the fully coupled and fully decoupled states, the intermediate states could be either: (i) sampled with an optimal frequency distribution (the sampling problem) or (ii) selected with an optimal spacing distribution (staging problem). The sampling issue is addressed by determining the biasing weights that would allow generating an optimal ensemble; discretized versions of this algorithm (well suited for small number of coupling stages) are also presented. The staging problem is addressed by selecting the intermediate stages in such a way that a flat histogram is the optimized ensemble. The validity of the advocated methods is demonstrated by their application to two model problems, the solvation of large hard spheres into a fluid of small and large spheres, and the vapor-liquid equilibrium of a chain system.

Year:  2007        PMID: 17994804     DOI: 10.1063/1.2800321

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


  2 in total

Review 1.  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

2.  Behavior of the Enthalpy of Adsorption in Nanoporous Materials Close to Saturation Conditions.

Authors:  Ariana Torres-Knoop; Ali Poursaeidesfahani; Thijs J H Vlugt; David Dubbeldam
Journal:  J Chem Theory Comput       Date:  2017-06-09       Impact factor: 6.006

  2 in total

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