A method to apply bond‐angle constraints in molecular dynamics simulations. Issue 6 (22nd December 2020)

• Record Type: Journal Article
• Authors: Pechlaner, Maria; Dorta, Andreas P.; Lin, Zhixiong; Rusu, Victor H.; van Gunsteren, Wilfred F.
• Is Part Of: Journal of computational chemistry. Volume 42:Issue 6(2021)
• Page Start: 418
• Page End: 434
• Publication Date: 2020-12-22
• Subjects: bond angles -- constraints -- Lagrange multipliers; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26466
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract: 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. Abstract : The bond‐angle constraint (BAC) algorithm maintains a constrained bond angle of three particles i, j and k, in a dynamics simulation by controlling the angle instead of relying on constraining the distance (DC) between the particles i and k, while solving Newton's or Langevin's equations of motion.