Self-assembly simulations with the C8S3 CG model were performed in which randomly positioned molecules were solvated in cubic boxes filled with water and counter ions. The goal of these simulations was to study the early steps of nucleation, the morphology of the formed aggregates and the local arrangement of the C8S3 monomers, when small clusters are formed. Four systems were prepared with different numbers of molecules (50, 100, 500 and 1000 C8S3) and different box sizes. More details for each system are reported in Table of the Supplementary Information. All systems were analysed in terms of aggregate formation and local arrangement of the monomers with respect to each other.