Vienna Soil Organic Matter Modeler 2

Explore an unknown environment.

The Vienna Soil Organic Modeler 2 is an online tool to create condensed phase models of humic substances.

Details about the modeler and examples of subsequent molecular dynamics simulations can be found in:
  • E. Galicia-Andrés, C. Oostenbrink, M.H. Gerzabek and D. Tunega
    On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure, Minerals (2021) 11, 1138
    doi: 10.3390/min11101138

  • Y. Escalona, D. Petrov and C. Oostenbrink
    Vienna Soil Organic Matter Modeler 2 (VSOMM2), J. Mol. Graph. Model. (2021) 103, 107817
    doi: 10.1016/j.jmgm.2020.107817

  • Y. Escalona, D. Petrov and C. Oostenbrink
    Modeling Soil Organic Matter: Changes in Macroscopic Properties due to Microscopic Changes, GCA (2021) 307, 228-241
    doi: 10.1016/j.gca.2021.05.035

  • Drazen Petrov, Daniel Tunega, Martin H. Gerzabek and Chris Oostenbrink
    Molecular Dynamics Simulations of the Standard Leonardite HumicAcid: Microscopic Analysis of the Structure and Dynamics, Environ. Sci. Technol. (2017), 51(10), 5414–5424 doi: 10.1021/acs.est.7b00266

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

Three different modes are available:

The basic input
This mode allows to specify the mass fraction of carbon and nitrogen, as well as the pH.

The 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).

The 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.

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.