We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.