To demonstrate the capability of the new protocol, we analyzed coarse-grained SOM models with varying compositions. The calculation of the potential energies of the non-bonded interactions indicated that the Coulomb interactions acted as the driving force for the packing of the SOM structures, which correlated with the acidity of the SOM systems. A subdivision of the Lennard-Jones interactions provided insight into how interactions changed with increasing water content. Exploring the larger length scales and longer simulation times revealed a local phase separation process, notably the formation of SOM voids, demonstrating the advantages of the coarse-graining approach.