One of the cyanine dyes that has been extensively studied the past decades is 5,5',6,6'tetrachloro-benzimida-carbocyanine (see Figure ). Several molecules with this specific core and different substituents have been designed and synthesised, and their structural and optical properties have been examined . Interestingly, different types of aggregates were formed ranging from bilayers and ribbons, to wires and nanotubes, depending on the chemical nature of the substituents and the experimental conditions. In this study, we were interested in 1,1'-dioctyl-3,3'-bis(2-sulfopropyl)-5,5',6,6'-tetrachloro-benzimida-carbocyanine (C8S3) (see Figure ), which forms double-walled nanotubes (see Figure ). C8S3 aggregates have been previously studied with MD simulation by testing the stability of different types of aggregates and their optical properties . These studies were limited to simulations of preformed aggregates, that do not necessarily allow the molecules to rearrange and explore a large portion of the available configurational space.