MOLECULAR-DYNAMICS ALGORITHM FOR FLEXIBLE MOLECULES USING NORMAL COORDINATES

A new algorithm for the treatment of flexible molecules in molecular dynamics simulation is presented. The equations of motion are formulated in terms of centre-of-mass position, quaternions, normal coordinates, and the corresponding momenta. Advantage is taken of the nearly harmonic motion of the normal coordinates by employing special purpose methods devised for the integration of trigonometric functions. Compared to simulations using Cartesian coordinates, much larger time steps can be used without affecting energy conservation. The algorithm is applied to liquids of diatomic molecules resembling nitrogen and to a model for liquid carbon tetrachloride. A time step acceptable for most applications turns out to be nearly independent of the internal frequencies involved, and is of the same size as is appropriate for the rigid molecule case.