VSOMM2 - About
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_vsomm.mtb (Contains all SOM building blocks as well as start and end groups for them)
54a7.ifp (Contains the necessary parameters)
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_vsomm.mtb (Contains all SOM building blocks as well as start and end groups for them)
54a7.ifp (Contains the necessary parameters)
Technology used for the webserver:
PYTHON
Bootstrap
3Dmol.js
intro.js
Technology used for the modeler:
PYTHON
GROMOS
SMArt