Collective mode mining from molecular dynamics simulations: a comparative approach

TL;DR

This paper compares various methods for extracting collective modes from molecular dynamics simulations, emphasizing their differences and complementarities in analyzing anharmonic and out-of-equilibrium systems like graphene and C60.

Contribution

It provides a comprehensive review and comparative analysis of methods for collective mode extraction, applied to complex molecular systems.

Findings

Different methods highlight distinct aspects of collective excitations.

Comparison reveals complementary insights into system behavior.

Approach aids in understanding anharmonic and non-equilibrium dynamics.

Abstract

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.