A Martini-based coarse-grained soil organic matter model derived from atomistic simulations

15 March 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The significance of soil organic matter (SOM) in environmental contexts, particularly its role in pollutant adsorption, has prompted increased utilization of molecular simulations to understand microscopic interactions. This study introduces a coarse-grained SOM model, parametrized within the framework of the versatile Martini 3 force field. Utilizing systems generated by the Vienna Soil Organic Matter Modeler 2, which constructs humic substance systems from a fragment database, we employed Swarm-CG to parametrize the fragments and subsequently assembled them into macromolecules. Direct Boltzmann Inversion (DBI) facilitated the determination of bonded parameters between fragments. The parametrization yielded favorable agreement in the radius of gyration and solvent-accessible surface area. Transfer free energies exhibited a strong correlation with hexadecane-water and chloroformwater values, albeit deviations were noted for octanol-water values. Comparing densities of modeled Leonardite Humic Acid (LHA) systems at coarse-grained and atomistic levels revealed promising agreement, particularly at higher water concentrations. The DBI approach effectively reproduced average values of bonded interactions between fragments. Radial distribution functions between carboxylate groups and calcium ions partially concurred, yet limitations arose in reproducing certain peaks due to fixed bead sizes. Detailed analysis of atomistic systems elucidated different configurations between groups, further explaining discrepancies. The present contribution provides a comprehensive insight into the properties, strengths, and weaknesses of the coarse-grained SOM model, serving as a foundation for future investigations encompassing pollutant interactions and varied SOM compositions.


coarse-grained molecular dynamics
soil organic matter

Supplementary materials

Supporting Information A Martini-based coarse-grained soil organic matter model derived from atomistic simulations
Additional information concerning Martini mapping


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