QM methods were used to obtain different sets of parameters, whose performance was evaluated in atomistic simulations. Specifically, the atomistic model was optimised in terms of bonded potentials of the aromatic core linker and partial charges (see Figure and). Optimisation was required in the dihedral angles of the polymethine bridge to ensure that the large conjugated system of the cyanine dyes is adequately described and can be used for different cyanine dyes. The torsional potentials that describe the dihedral angles of the linker have been determined based on the energy difference between the QM and the MD dihedral profiles using Q-force . For the partial charges, the Dipole Preserving Analysis (DPA) using the GAMESS-UK software , and the Restricted Electrostatic Potential (RESP) method using the Gaussian16 software were used to obtain different sets of parameters and test their performance. The procedure for obtaining parameters and the final comparison are included in Table -S3 and Figure of the Supplementary Information.