Reactive molecular dynamics: From small molecules to proteins

Abstract

The current status of reactive molecular dynamics (MD) simulations is summarized. Both, methodological aspects and applications to problems ranging from gas phase reaction dynamics to ligand-binding in solvated proteins are discussed, focusing on extracting information from simulations that cannot easily be obtained from experiments alone. One specific example is the structural interpretation of the ligand rebinding time scales extracted from state-of-the art time-resolved experiments. Atomistic simulations employing validated reactive interaction potentials are capable of providing structural information about the time scales involved. Both, merits and shortcomings of the various methods are discussed and the outlook summarizes possible future avenues such as reactive potentials based on machine learning techniques. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics Molecular and Statistical Mechanics > Molecular Interactions.