First, we calculated the number of clusters as a function of time, since this measurement gives an estimate of how fast the monomers aggregate, and whether the clusters merge to form larger structures. The number of clusters in each system was calculated by measuring the number of molecules within a certain cut-off distance. If the central beads of the aromatic core (TC4, Figure ) of the monomers were within 1.5 nm, the molecules were accounted to be in the same cluster. In smaller systems, a cluster was rapidly formed and was maintained along the trajectory (see Figure ). A similar behaviour was also observed in the larger systems, but a single aggregate was not formed. Instead, the C8S3 molecules aggregated into several large clusters that did not merge during the simulated time scales. Both observations suggest that the hydrophobic effect is dominant in the beginning of the C8S3 self-assembly process, since the molecules immediately collapse into different structures, in which the alkyl tails are concealed from water. However, as the size of the aggregates increases, their fusion becomes slower. This behaviour could be attributed to the high energy barrier that prevents large aggregates from merging and keeping them kinetically trapped in worm-like structures. Snapshots from the last frames of each system show that the small systems formed small spherical blobs and the large systems formed elongated structures (Figure ). No aggregate formation similar to the tubular structures that are reported in the experiments was observed during our simulations. There are several reasons that could justify the different observations between the simulations and the experiments, such as the C8S3 concentration that was significantly larger in the simulations, the different timescales that diverge several orders of magnitude or the system sizes. These reasons are partially interconnected, and they highlight the complexity of simulating random self-assembly processes with either fine or coarse molecular models. To study the local arrangement inside the aggregates, the radial distribution function (RDF) of the central beads and the relative orientation of each monomer were measured at different time steps of the trajectories. Our results show that the local arrangement of the monomers is quite similar in all self-assembly simulations. Specifically, most of the molecules are located at a distance of either ∼0.4 nm or ∼0.8-0.9 nm (see Figure ). The relative orientation of the C8S3 molecules was described as a function of distance and angles between each monomer (see Figure ). To calculate the angles, the aromatic cores were represented as vectors defined by the position of the dummy particles (see Figure ). Three different formations are used as reference: staircase (SC), brickwork (BW) and herringbone (HB). Molecule pairs at a distance of ∼0.8 nm could indicate either BW or HB arrangements, but the relative orientation analysis shows that the BW arrangement is preferred, since the angle between the vectors is ∼10 • (see Figure ). At ∼0.4 nm distance, the molecules arrange in a SC formation. SC arrangements are characteristic in self-assembled aggregates that present blue-shifted absorption spectra compared to the absorption of the solvated monomers . The C8S3 nanotubes present red-shifted absorption spectra indicating a BW or HB formation of the monomers in the final structures, but there is no evidence showing that C8S3 do not undergo a wide search of possible conformations during their self-assembly. The same analyses were performed at different time steps of the simulations, but the results are roughly the same in all systems (see Figures of the Supplementary Information). This indicates that the preferred packing mode of the C8S3 molecules is already adopted at an early stage of the self-assembly process.