  The evaluation of collective modes is fundamental in the analysis of
molecular dynamics simulations. Several methods are available to extract that
information, i.e normal mode analysis, principal component and spectral
analysis of trajectories, basically differing by the quantity considered as the
nodal one (frequency, amplitude, or pattern of displacement) and leading to the
definition of different kinds of collective excitations and physical spectral
observables. Different views converge in the harmonic regime and/or for
homo-atomic systems. However, for anharmonic and out of equilibrium dynamics
different quantities bring different information and only their comparison can
give a complete view of the system behavior. To allow such a comparative
analysis, we review and compare the different approaches, applying them in
different combination to two examples of physical relevance: graphene and
fullerene C60.
