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Method for free‐energy calculations using iterative techniques
Author(s) -
Kumar Shankar,
Payne Philip W.,
Vásquez Maximiliano
Publication year - 1996
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/(sici)1096-987x(19960730)17:10<1269::aid-jcc7>3.0.co;2-m
Subject(s) - ramachandran plot , histogram , extension (predicate logic) , iterative method , energy (signal processing) , computer science , algorithm , mathematics , physics , statistics , artificial intelligence , nuclear magnetic resonance , protein structure , image (mathematics) , programming language
We present here a new iterative technique for reliable estimation of multidimensional free energy and potential of mean force (PMF) values by computer simulation. This method is an extension of the weighted histogram analysis method [S. Kumar et al., J. Comput. Chem., 13, 1011, (1992)]. We have tested the technique by generating free‐energy‐based Ramachandran plots and by computing the PMF values for end‐to‐end distances for several polypeptides using the ECEPP/2 and AMBER force fields. © 1996 by John Wiley & Sons, Inc.