All simulations were performed with the GROMACS 2018 simulation package . For the atomistic simulations, an extended version of the GROMOS force field version G54a7 36 was used that incorporates recent parameters for molecules from the ATB database and can be found on the ATB website (). In this version, there is an additional atom type for carbons in aromatic rings (CAro) that was used for representing the carbons of the cyanine core. Furthermore, parameters for iodine (ATB Molecule ID:337757), DMSO (ATB Molecule ID:1202) and methanol (ATB Molecule ID:15607), that were present in the crystal structures of the cyanine dyes, were downloaded from the ATB database. Simulations with solvated cyanine dyes in water were used to obtain distributions for the bonded terms of the CG model. In those cases, explicit SPC water molecules were used to model water and counter ions (Na + ) were introduced to neutralise the systems.