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Some recent techniques for free energy calculations
Author(s) -
VandenEijnden Eric
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21332
Subject(s) - voronoi diagram , energy landscape , tessellation (computer graphics) , context (archaeology) , energy (signal processing) , set (abstract data type) , statistical physics , kinetic energy , potential energy , molecular dynamics , centroidal voronoi tessellation , computer science , algorithm , physics , mathematics , classical mechanics , geometry , quantum mechanics , thermodynamics , geology , programming language , paleontology
A few recent techniques to calculate free energies in the context of molecular dynamics simulations are discussed: temperature‐accelerated molecular dynamics, which is a method to explore fast the important regions in the free energy landscape associated with a set of continuous collective variables without having to know where these regions are beforehand; the single sweep method, which is a variational method to interpolate the free energy globally given a set of mean forces (i.e., a set of gradients of the free energy) calculated at specific points, or centers, on the free energy landscape; and a Voronoi‐based free energy method for the calculation of the free energy of the Voronoi tessellation associated with a set of centers. We also discuss how this last technique can be used in conjunction with the string method, and how kinetic information such as reaction rates can be calculated by milestoning using the edges of a Voronoi tessellation as milestones. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009