We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4 x 4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.