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Multidimensional free‐energy calculations using the weighted histogram analysis method
Author(s) -
Kumar Shankar,
Rosenberg John M.,
Bouzida Djamal,
Swendsen Robert H.,
Kollman Peter A.
Publication year - 1995
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.540161104
Subject(s) - histogram , umbrella sampling , potential of mean force , monte carlo method , force field (fiction) , representation (politics) , extension (predicate logic) , potential energy , potential energy surface , statistical physics , algorithm , computer science , mathematics , computational chemistry , chemistry , physics , molecular dynamics , statistics , quantum mechanics , molecule , artificial intelligence , politics , political science , law , image (mathematics) , programming language
The recently formulated weighted histogram analysis method (WHAM) 1 is an extension of Ferrenberg and Swendsen's multiple histogram technique for free‐energy and potential of mean force calculations. As an illustration of the method, we have calculated the two‐dimensional potential of mean force surface of the dihedrals gamma and chi in deoxyadenosine with Monte Carlo simulations using the all‐atom and united‐atom representation of the AMBER force fields. This also demonstrates one of the major advantages of WHAM over umbrella sampling techniques. The method also provides an analysis of the statistical accuracy of the potential of mean force as well as a guide to the most efficient use of additional simulations to minimize errors. © 1995 John Wiley & Sons, Inc.