Details about the modeler can be found in:

• Vienna Soil Organic Matter Modeler 2 (VSOMM2), Y. Escalona, D. Petrov and C. Oostenbrink, J. Mol. Graphics Model. (2021), 103, 107817 doi: 10.1016/j.jmgm.2020.107817
  
• Vienna Soil Organic Matter Modeler - Generating condensed-phase models of humic substances, A. Sündermann, R. Solc, D. Tunega, G. Haberhauer, M.H. Gerzabek and C. Oostenbrink, J. Mol. Graph. Model. (2015), 62, 243-261 doi: 10.1016/j.jmgm.2015.10.007
  
  

Three different modes are available:
Basic input
This mode allows to specify the mass fraction of carbon and nitrogen, as well as the pH.
Advanced input
With this mode, for the carbon atoms, the requested fractions of functional groups can be defined (Carbonyl-C, Carboxyl-C, O-aryl, Aryl, Di-O-Alkyl, O-Alkyl, Methoxyl and Alkyl-C).
Random input
This mode produces a random model of the given size based on the specified random seed.

The time the generation process takes is very dependent on the system size. Large systems need considerably longer than smaller systems. For very large systems, a smaller molecule size should be considered.

Output
After model generation, a report, a GROMOS topology, a GROMOS coordinate file and a PDB can be downloaded.
The structure is at a density of 500 kg/m³, and needs to be condensed further in an offline step.