Premium
Symmetrization of the AMBER and CHARMM force fields
Author(s) -
Małolepsza Edyta,
Strodel Birgit,
Khalili Mey,
Trygubenko Semen,
Fejer Szilard N.,
Wales David J.
Publication year - 2010
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.21425
Subject(s) - symmetrization , force field (fiction) , computational chemistry , chemistry , force constant , nucleic acid , symmetry (geometry) , kinetic energy , statistical physics , mathematics , physics , classical mechanics , quantum mechanics , molecule , combinatorics , geometry , organic chemistry , biochemistry
The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010