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A method to apply bond‐angle constraints in molecular dynamics simulations
Author(s) -
Pechlaner Maria,
Dorta Andreas P.,
Lin Zhixiong,
Rusu Victor H.,
Gunsteren Wilfred F.
Publication year - 2021
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.26466
Subject(s) - dihedral angle , cartesian coordinate system , molecular dynamics , molecular geometry , bond length , lagrange multiplier , computer science , physics , algorithm , classical mechanics , molecule , mathematics , mathematical optimization , computational chemistry , geometry , chemistry , quantum mechanics , hydrogen bond
An algorithm to apply bond‐angle constraints in molecular dynamics simulations of macromolecules or molecular liquids is presented. It uses Cartesian coordinates and determines the Lagrange multipliers required for maintaining the constraints iteratively. It constitutes an alternative to the use of only distance constraints (DCs) between particles to maintain a particular geometry. DCs are unsuitable to maintain particular, for example, linear or flat, geometries of molecules. The proposed algorithm can easily handle bond‐length, bond‐angle, and dihedral‐angle constraints simultaneously, as when calculating a potential of mean force along a dihedral‐angle degree of freedom.