In the framework of a classical MD simulation, "topology" describes the identities of each atom and their covalent connectivity in the system. The atomic identities are extensive; for instance, the CHARMM36 protein force field has 20 different types of carbon where each atom type has unique parameters for the partial charge, bond lengths, and rotation around chemical bonds. A harmonic energy function defines the bonds between atoms, which can vibrate around a minimum energy position but can never break. The system's topology for the classical MD simulation is thus determined at the beginning of the simulation and remains fixed for the duration of a trajectory.