A molecular model system of tetraphenyl porphyrins (TPP) adsorbed on metallicsubstrates is systematically investigated within a joint scanning tunnellingmicroscopy/molecular modelling approach. The molecular conformation of TPP molecules,their adsorption on a gold surface and the growth of highly ordered TPP islands aremodelled with a combination of density functional theory and dynamic force fieldmethods. The results indicate a subtle interplay between different contributions. Themolecule–substrate interaction causes a bending of the porphyrin core whichalso determines the relative orientations of phenyl legs attached to the core. Amajor consequence of this is a characteristic (and energetically most favourable)arrangement of molecules within self-assembled molecular clusters; the phenyl legsof adjacent molecules are not aligned parallel to each other (often denoted asπ–π stacking) but perpendicularly in a T-shaped arrangement. The results of the simulationsare fully consistent with the scanning tunnelling microscopy observations, in terms of thesymmetries of individual molecules, orientation and relative alignment of molecules in theself-assembled clusters.