Hierarchic construction of a general particle in brownmove. The top level "Protein" object contains one or more "Gestalt" objects which move independently and contain a shape for each interaction, which in turn contains the basic interaction entities. These are point charges for electrostatic interactions or van-der-Waals spheres for effective short range interactions. With these the forces acting on the Gestalt are calculated. The "GeomShape" object is always present and handles the conversion of the forces into a respective displacement.
Geyer BMC Biophysics 2011 4:7 doi:10.1186/2046-1682-4-7