Pd particles supported on the MgO(001) surface were simulated by the molecular dynamics (MD) method. The surface and inner structures of the particles as well as the interaction sites of the Pd atoms were investigated by using computer graphics (CG) techniques. The numerical features of the surface atomic rows, the inplane symmetric configurations, the height deviation of the layer, and the lattice length defined by the distance between near neighboring rows were estimated. The dependency and the interdependence of these atomistic characteristics were evaluated. The findings on the lattice spaces were compared with the experimental and other theoretical calculation results.