We present molecular dynamics simulations (MDS) for interpreting the molecular aggregation of four different asphaltene molecular models. These simulations are based on recent small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) experiments from Eyssautier and co-workers [Eyssautier, J.; Levitz, P.; Espinat, D.; Jestin, J.; Gummel, J.; Grillo, I.; Barre, L. Insight into asphaltene nanoaggregate structure inferred by small angle neutron and X-ray scattering. J. Phys. Chem. B 2011, 115 (21), 6827-6837, 10.1021/jp111468d], which proposed a discoidal asphaltene nanoaggregate structure of 0.67 nm height and its chemical composition. Basically, we have investigated the sulfur atom position in the asphaltene structure. pi-pi is the main type of contact, and it seems to be responsible for the parallel orientation of molecules. This geometry is also corroborated by the cosine of angles between the polyaromatic cores. However, the polar side chain is also important to the aggregation, because it occurs in the systems during all of the simulations. Three systems, namely, systems 1T, 2T, and 4T, are in good agreement with experimental work, indicating an average height lower than 0.8 nm. Concerning the place occupied by the sulfur atom in the molecule, we have found that, when it is grafted directly to the conjugated core, no effect can be deducted from the stability of dimers and trimers and all of the other studied parameters. This is not the case when sulfur is located in the lateral chain, where it has a particular affinity with oxygen and hydrogen atoms of the acid chain ends of neighboring molecules. Consequently, we suggest that these configurations of the sulfur atom are more likely to be problematic in the oil industry.