DYNAMICAL ANALYSIS OF LINEAR-POLYMERS USING MODE-SPECIFIC TRAJECTORIES

Recently, a new method was presented for calculating vibrational dispe rsion curves for linear polymers from the spectral analysis of molecul ar dynamics trajectories with random initial conditions. An alternativ e approach is to choose initial conditions for trajectories such that only one collective mode corresponding to a specific vibrational frequ ency and phase relationship is preferentially excited. As a result, fo r the first time all the standard techniques of nonlinear dynamics (Li ssajous figures, surfaces of section, etc.) may be applied to the coll ective coordinates of a macromolecule. After demonstrating that approx imate initial conditions will preferentially excite specific collectiv e modes, improved dispersion curves for a 100 unit all-trans polyethyl ene chain are compared with the results of a normal coordinate analysi s. The similarity of the phase space of collective modes and local mod es is then shown through plots of Lissajous figures and surfaces of se ction for trajectories in which multiple collective modes are excited simultaneously.