While such systems consisting of larger, supramolecular structures can improve the accuracy of the model, the accessible time and length scales of simulations may be compromised. One way to enhance their performance is through the coarse-graining approach , whereby groups of atoms are combined into larger particles, known as beads. This eliminates finer interaction details but can speed up the simulations by two orders of magnitude. We have therefore developed a tool that converts VSOMM2 systems from an atomistic to a coarse-grained representation, using the Martini 3 framework 60 . On the one hand, this enables an abstraction of the SOM molecular structures, whose exact shape remains unknown, and on the other hand, the simulation of diffusion processes and large SOM systems while accounting for the heterogeneous interaction sites of SOM. To the best of our knowledge, no molecular-level study has examined the interaction between pollutants and supramolecular SOM structures over extended time scales, with a focus on their diffusion and distinct interaction sites.