BackgroundSpatial computer simulations are becoming more feasible and relevant for studies of signaling pathways due to technical advances in experimental techniques yielding better high resolution data. However, many common single particle simulation environments used in computational systems biology lack the functionality to easily implement spatially heterogeneous membrane environments.ResultsWe introduce an extension to the single particle simulator Smoldyn that allows modeling of surface-dependent diffusion, without unnecessarily increasing molecular states or numbers, hence avoiding explosion of molecule and reaction definitions.ConclusionsWe demonstrate the usefulness of this approach studying AMPA receptor diffusion at the postsynaptic density and its spatial trapping without introducing hypothetical scaffold elements or membrane barriers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1723-6) contains supplementary material, which is available to authorized users.