In molecular dynamics, atoms interact with each other. These interactions originate forces which act upon atoms, and atoms move under the action of these instantaneous forces. As the atoms move, their relative positions change and forces change as well.
The essential ingredient containing the physics is therefore constituted by the forces. A simulation is realistic--that is, it mimics the behavior of the real system--only to the extent that interatomic forces are similar to those that real atoms (or, more exactly, nuclei) would experience when arranged in the same configuration.
As described in 2.1, forces are usually obtained as the gradient of a potential energy function, depending on the positions of the particles. The realism of the simulation therefore depends on the ability of the potential chosen to reproduce the behavior of the material under the conditions at which the simulation is run.
The problem of selecting--or constructing--potentials is addressed in more detail in chapter 4.