Dynamical analysis of linear polymers using mode-specific trajectories

Recently, a new method was presented for calculating vibrational dispersion curves for linear polymers from the spectral analysis of molecular dynamics trajectories with random initial conditions. An alternative approach is to choose initial conditions for trajectories such that only one collective mode corresponding to a specific vibrational frequency and phase relationship is preferentially excited.As a result, for the first time all the standard techniques of nonlinear dynamics (Lissajous figures, surfaces of section, etc.) may be applied to the collective coordinates of a macromolecule. After demonstrating that approximate initial conditions will preferentially excite specific collective modes, improved dispersion curves for a 100 unit all-trans polyethylene chain are compared with the results of a normal coordinate analysis. The similarity of the phase space of collective modes and local modes is then shown through plots of Lissajous figures and surfaces of section for trajectories in which multiple collective modes are excited simultaneously.