Sh. Lee et al., New out-of-plane angle and bond angle internal coordinates and related potential energy functions for molecular mechanics and dynamics simulations, J COMPUT CH, 20(10), 1999, pp. 1067-1084
With currently used definitions of out-of-plane angle and bond angle intern
al coordinates, Cartesian derivatives have singularities, at +/- pi/2 in th
e former case and pi in the latter. If either of these occur during molecul
ar mechanics or dynamics simulations, the forces are not well defined. To a
void such difficulties, we provide new out-of-plane and bond angle coordina
tes and associated potential energy functions that inherently avoid these s
ingularities. The application of these coordinates is illustrated by nb ini
tio calculations on ammonia, water, and carbon dioxide. (C) 1999 John Wiley
& Sons, Inc.