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Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles
Author(s) -
Gibson Kenneth D.,
Scheraga Harold A.
Publication year - 1990
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.540110407
Subject(s) - dihedral angle , kinetic energy , potential energy , computation , pairwise comparison , function (biology) , molecular dynamics , interatomic potential , geometry , energy (signal processing) , classical mechanics , mathematics , mathematical analysis , computational chemistry , physics , chemistry , algorithm , quantum mechanics , molecule , hydrogen bond , statistics , evolutionary biology , biology
Expressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.