4. Molecular dynamics

4.1 Definitions

The principle of a molecular dynamics simulation is to animate atoms, a molecule or a set of objects, leading to a trajectory, i.e. a sequence of configurations over time. As we shall see in paragraph 4.5.1 , this corresponds to the exploration of phase space. This trajectory contains the coordinates and quantities of motion of all atoms, enabling appropriate analyses to be carried out, such as temperature, pressure and autocorrelation function calculations