These programs are classical 2-dimensional molecular dynamics simulations. Such simulations compute the motions of atoms by summing (integrating) all of the forces that the atoms exert on each other. These forces arise from changes in potential energy that depend on the separation distances between the atoms. In principle each atom is interacting with all of the other atoms in the simulation, and thus the forces must be computed between every possible pair of atoms in the simulation. Once the net force is computed for each atom, it's position and velocities are updated and the procedure is repeated.