An efficient scheme is developed to study magnetism and structure as well as interaction between supported particles on the atomic scale. Starting by ab initio calculations of the electronic structure in the framework of density functional theory, interaction potentials for molecular dynamics simulations of metallic nanostructures supported on metallic surfaces are carefully optimized. The two methods are shortly explained. Examples for the application of the methods are given. Mainly electronic and structural properties of Co nanostructures on Cu(001) and Cu(111) surfaces are investigated.