Guiding mode analysis, a generalization of normal mode analysis

Abstract

A new approach is presented to investigating collective periodic motion in molecules, analyzing the Fourier transforms of molecular dynamics simulation trajectories. Demanding that atoms vibrating together in some mode must oscillate in phase enables the corresponding collective coordinate to be deduced. We demonstrate that the method for purely harmonic potentials gives results identical to conventional normal mode analysis. It can, however, be applied to any molecular dynamics simulation trajectory, probing anharmonic regions of the potential, with solvent explicitly included, in non-equilibrium situations.