Some studies on generalized coordinate sets for polyatomic molecules.

Abstract

Generalized coordinates are widely used in various analyses of the trajectories of polyatomic molecules from molecular dynamics simulations, such as normal mode analysis and force distribution analysis. Here, we presented detailed discussions on the properties of some specific sets of generalized coordinates, which separate translational, rotational, and vibrational motions of a molecule from one another once the trajectories of dynamical systems are known. Efficient methods were suggested for estimating the transformation matrix between generalized and Cartesian coordinates. Some properties of the well-known BAT coordinates (bond length, angle, and torsional coordinates) were discussed as well.