Welcome to the Vienna Soil Organic Matter Modeler!
The Vienna Soil Organic Modeler 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:
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
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
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.
|Example of a system create with this tool.|
Vienna Soil Organic Matter Modeler Basic Input
|This is the basic input mask|
Vienna Soil Organic Matter Modeler Advanced Input
|This is the advanced input mask|
Vienna Soil Organic Matter Modeler Random Input
|This is the random input mask|
Vienna Soil Organic Matter Modeler
The Vienna Soil Organic Matter Modeler is an online tool designed to create condensed
phase models of soil organic matter in a two step process.
The first step is the online modeling tool and the second step consists of an offline thermolization, compression and equilibration of the model.
The online modeling tool is split up into a frontend web application and a backend modeler.
It is developed at the Institute of Molecular Modeling and Simulation of University of Natural Resources and Life Sciences in Vienna.
The Vienna Soil Organic Matter Modeler uses a database of currently 34 larger fragments, the so called building blocks to generate the soil organic matter models. The parameters needed to describe the interactions and dynamics of the building blocks are derived from the GROMOS force field 54A7 (Schmid et.al.).
The full force field files can be downloaded here:
54a7.mtb (Contains all 34 SOM building blocks as well as start and end groups for them)
54a7.ifp (Contains the necessary parameters)
Responsible for the contents:
Institute of Molecular Modeling and Simulation - University of Natural Resources and Life Sciences, Vienna
The Vienna Soil Organic Matter Modeler generates automated theoretical models without any human intervention during the entire process. The result is non-experimental and therefore must be considered with care as the generated models may contain significant errors. All information on this site is provided "as-is", without any warranty, expressed or implied.
Copyright and fair use
The Vienna Soil Organic Matter Modeler is developed at the Institute of Molecular Modeling and Simulation of University of Natural Resources and Life Sciences in Vienna. The Vienna Soil Organic Matter Modeler program, website, logo, name and models produced by it are copyright. When you publish or patent results which were fully or partially based on models created with the Vienna Soil Organic Matter Modeler, please cite the corresponding publications.