Vienna soil organic matter modeler 2 (VSOMM2)

Abstract

Soil Organic Matter (SOM) plays an important role in several biogeochemical processes by directly affecting the microbial activity, soil aggregation, plant growth and carbon storage. Despite of its importance, our understanding of its composition and structure is still incomplete. Several experiments using elemental analysis, nuclear magnetic resonance (NMR) and mass spectrometry (MS) shed light on the structure of organic matter. In this context, the Vienna Soil-Organic-Matter Modeler (https://somm.boku.ac.at/) is a website that generates condensed phase computer models of Soil-Organic-Matter (SOM). Most of the data comes from standardized samples by the International Humic Substances Association (IHSS), which uses a specific methodology to extract organic compounds from soil, called humic substances. We have improved the modeler by increasing the pool of elemental units that compose our SOM molecules called building blocks, and also by implementing a genetic algorithm that increases the chemical and geometric diversity of the models. This allowed us to create models using the IHSS data as well as different types of soil. The webserver uses as an input principally the elemental and organic composition and offers input files needed to run molecular dynamic (MD) simulations of solvated and neutralized SOM within the framework of the GROMOS 54A7 forcefield and the GROMOS and GROMACS simulation packages.

Keywords: GROMOS; Humic substances; In silico modeling; Molecular dynamics.