Cyanine dyes are a family of molecules whose members are known to aggregate and form different types of structures with discrete features . A typical structure of a cyanine dye contains a polymethine bridge, a chain with an odd number of methine groups (=CH-) connected via alternating single and double bonds, with nitrogen atoms on both ends (see Figure ). The conjugated system created by the pi-orbitals of the polymethine bridge provides a chromophore responsible for the optical signature of each cyanine dye. In different solvents, cyanine dyes form organised structures that exhibit different optical properties compared to the solvated monomers. Such special optical properties were first reported for the pseudoisocyanine (PIC) dye . Later, it was suggested that the strong coupling of the individual molecules was responsible for the spectral changes, which depend on the structure of the aggregates and the relative orientation of the monomers . Understanding the driving forces that govern the formation of specific structures and the monomer arrangement inside the aggregates is of major importance in order to design molecules with specific chemical features and, ultimately, predict their supramolecular structures and properties. Computational modelling, in particular molecular dynamics (MD) simulations, are a powerful tool to aid in the rational design process of supramolecular biomolecules and nanomaterials .