The most important output of an MD simulation (see Sect. 2.3) is a trajectory that contains the coordinates of all atoms in each simulation step. When there are M atoms, this is a path through the 3 M-dimensional configuration space of the system. Since this high-dimensional object is not directly accessible for interpretation and extraction of chemical characteristics, methods to reduce the dimensionality need to be applied. These can be simple structural analyses such as, eg, radial pair distribution functions, or more involved dynamical analyses