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New out‐of‐plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations
Author(s) -
Lee SangHo,
Palmo Kim,
Krimm Samuel
Publication year - 1999
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(19990730)20:10<1067::aid-jcc9>3.0.co;2-v
Subject(s) - gravitational singularity , cartesian coordinate system , plane (geometry) , curvilinear coordinates , molecular geometry , bipolar coordinates , molecular dynamics , physics , classical mechanics , rotation (mathematics) , log polar coordinates , polar coordinate system , orthogonal coordinates , generalized coordinates , computational chemistry , geometry , chemistry , mathematics , quantum mechanics , molecule
With currently used definitions of out‐of‐plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at ±π/2 in the former case and π in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid such difficulties, we provide new out‐of‐plane and bond angle coordinates and associated potential energy functions that inherently avoid these singularities. The application of these coordinates is illustrated by ab initio calculations on ammonia, water, and carbon dioxide. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1067–1084, 1999