The Radial Distribution Function (RDF) is an effective way of describing the average structure of disordered molecular systems such as liquids, but it is also helpful when looking at diordered (and ordered) solids. If you look at the atoms in the MD Engine, you can see how complicated the structure appears in terms of the atom positions and how they change withtime. One way in which we can analyse such structures effectively is to imagine how the average structure looks from the point of view of a single reference atom; this average is over time and over the other atoms in the system. The reference atom is effectively regarded as being in the centre of the structure. This experiment shows how the RDF is built up over time, during the course of a molecular dynamics simulation.