A method to apply bond-angle constraints in molecular dynamics simulations

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.

Automated summary

An algorithm is presented for applying bond-angle constraints in molecular dynamics simulations, using Cartesian coordinates and iterative determination of Lagrange multipliers. This method provides an alternative to using only distance constraints between particles, and can easily handle bond-length, bond-angle, and dihedral-angle constraints simultaneously.