The trees and the forest: Aims and objectives of molecular dynamics simulations

This comment presents few reflections, inspired by various contributions in this special issue, that address the issue of how to interpret and use molecular dynamics (MD). It is argued that, in spite of what its name seems to suggest, MD is not a tool to predict deterministic behaviors but a device to sample both time-independent and time-dependent statistical mechanics properties of molecular systems. Therefore MD simulations must be used in concert with tools from stochastic processes theory and a big challenge is how to develop these tools to make them appropriate both conceptually and practically in the context of these simulations.