In the broadest sense, molecular dynamics is concerned with molecular motion.
Motion is inherent to all chemical processes.
Simple vibrations, like bond stretching and angle bending, give rise to IR spectra. The driving force for chemical processes is described by thermodynamics . The mechanism by which chemical processes occur is described by kinetics . Molecular dynamics alters the intramolecular degrees of freedom in a step-wise fashion, analogous to energy minimization. The individual steps in energy minimization are merely directed at establishing a down-hill direction to a minimum.