Escalona Yerko, Petrov Drazen, Oostenbrink Chris
Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190, Vienna, Austria.
Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190, Vienna, Austria.
J Mol Graph Model. 2021 Mar;103:107817. doi: 10.1016/j.jmgm.2020.107817. Epub 2020 Nov 26.
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.
土壤有机质（SOM）通过直接影响微生物活性、土壤团聚、植物生长和碳储存，在多个生物地球化学过程中发挥着重要作用。尽管其很重要，但我们对其组成和结构的理解仍不完整。一些使用元素分析、核磁共振（NMR）和质谱（MS）的实验揭示了有机质的结构。在此背景下，维也纳土壤有机质建模器（https://somm.boku.ac.at/）是一个生成土壤有机质（SOM）凝聚相计算机模型的网站。大部分数据来自国际腐殖质协会（IHSS）的标准化样本，该协会使用一种特定方法从土壤中提取有机化合物，即腐殖质。我们通过增加构成我们称为构建块的SOM分子的元素单元库，以及通过实施一种增加模型化学和几何多样性的遗传算法，对建模器进行了改进。这使我们能够使用IHSS数据以及不同类型的土壤创建模型。该网络服务器主要将元素和有机组成作为输入，并提供在GROMOS 54A7力场以及GROMOS和GROMACS模拟包框架内运行溶剂化和中和的SOM分子动力学（MD）模拟所需的输入文件。
