Internal coordinate phase space analysis of macromolecular systems

In recent studies, as well as the results presented herein, it has been shown that the classical dynamics of macromolecular systems exhibit chaos far below the zero-point energy consequently resulting in the loss of a qualitative correspondence to quantum behavior. Mechanisms responsible for this undesirable 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 amplitude modes. A very powerful tool for eliminating the high frequency modes in macromolecular systems has been the development of internal coordinate molecular 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 eliminate most of the problems associated with zero-point energy flow and the resulting phase space structure exhibits a high degree of stable quasiperiodic motion. However, the semi-classical relationships to quantum mechanics in this quasiperiodic regime require that initial conditions be chosen carefully in order for the resulting trajectory to have any quantum relevance.