Simulations of biomolecular dynamics are commonly interpreted in terms of harmonic or quasi-harmonic models for the dynamics of the system.
Harmonic models assume that the molecule exhibit oscillations around one energy minimum.
However, experimental data suggest that the protein samples multiple minima and that transitions among minima shows a broad distribution of energy barriers. To elucidate the nature of the dynamics of a protein we have studied the molecular dynamics trajectories of various proteins in aqueous solution. These trajectories show that proteins sample multiple local energy minima. Transitions among minima involve collective motions of amino acids over long distances. We show that nonlinear motions are responsible for most of the atomic fluctuations of the protein.