Internal coordinate phase space analysis of macromolecular systems

In recent studies, as well as the results presented herein, it has been sho wn that the classical dynamics of macromolecular systems exhibit chaos far below the zero-point energy consequently resulting in the loss of a qualita tive correspondence to quantum behavior. Mechanisms responsible for this un desirable and unrealistic dynamics have been shown to be due to the flow of energy out of the high frequency modes into the low frequency, large ampli tude modes. A very powerful tool for eliminating the high frequency modes i n macromolecular systems has been the development of internal coordinate mo lecular dynamics. This method only integrates the chosen degrees of freedom that determine the overall structure of the molecular system (the torsion) . In this paper, we have used this technique with the appropriate analysis from semi-classical theory and nonlinear dynamics to study the trajectories generated for some simple polymer fragments. The method does effectively e liminate most of the problems associated with zero-point energy flow and th e resulting phase space structure exhibits a high degree of stable quasiper iodic motion. However, the semi-classical relationships to quantum mechanic s in this quasiperiodic regime require that initial conditions be chosen ca refully in order for the resulting trajectory to have any quantum relevance . (C) 2000 Published by Elsevier Science Ltd.