Classical molecular-dynamics simulations based on the Tersoff potential are used to compute at the atomic level the strain-induced potential well generated at the surface of the capping layer by a buried, three-dimensional Ge island on Si(001). A simple model is outlined in order to predict the configurational arrangement for the nucleation of small Ge islands in such a potential well. The theoretical predictions are compared with atomic force microscope images of multilayered SiGe nanostructures grown by chemical vapor deposition. The cluster configuration is shown to be strongly dependent on the capping layer thickness, and to closely mimic the behavior predicted by the model. (c) 2005 American Institute of Physics.