som2cg 0.13.0

Coarse-graining soil organic matter models to Martini 3

SOM2CG - Coarse-Graining Soil Organic Matter Models

A tool for converting atomistic soil organic matter (SOM) models from the Vienna soil organic matter modeler 2 (VSOMM2, https://somm.boku.ac.at) to a coarse-grained representation, compatible with the Martini 3 force field.

Prerequisites

The program is written in Python 3 and requires the packages mdanalysis, rdkit, and pyyaml. SOM2CG can be installed via pip:

pip install som2cg

Execution

You can execute the program in the directory with the topology files from the VSOMM2, or modify e.g. the directory paths using the following arguments:

som2cg [-V] [-h] [-nt 'number of threads'] 
       [-input_dir 'input directory'] 
       [-output_dir 'output directory'] 
       [-n_confs 'number of conformers']
       [-coords 'atomistic coordinate file']  
       [-map '"cog" or "com" mapping'] 
       [-parametrize '(yes/no) parametrize the molecules, or only output mapped structure file']
       [-solvate '(yes/no) solvate the mapped structure file']
       [-use_std_fc '(yes/no) use standard force constants']
       [-with_progress_bar '(yes/no) activate a progress bar']
       [-config 'YAML configuration file']

For example, the following command will use 4 threads to convert the atomistic topology files, located in the folder 'atomistic' with 500 conformers and solvate the coarse-grained system at the end:

som2cg -nt 4 -input_dir atomistic -n_confs 500 -solvate yes

You can decrease the number of conformers for testing to accelerate the parametrization step.

Contributing

If you have any suggestions for improving the efficiency of the program, or for additional features, feel free to contact one of the authors of the publication.

Citation and Acknowledgments

If you use SOM2CG, please cite the following papers:

Dettmann, L. F.; Kühn, O.; Ahmed, A. A. Automated Parametrization Approach for 
Coarse-Graining Soil Organic Matter Molecules. Journal of Chemical Theory and 
Computation, 2024, 20, 10684–10696. https://doi.org/10.1021/acs.jctc.4c01334.

Dettmann, L. F.; Kühn, O.; Ahmed, A. A. Martini-Based Coarse-Grained Soil Organic 
Matter Model Derived from Atomistic Simulations. Journal of Chemical Theory and 
Computation, 2024, 20, 5291–5305. https://doi.org/10.1021/acs.jctc.4c00332.

Parts of this code are based on work by Mark A. Miller and coworkers, used with permission. These parts are subject to the following citations:

Potter, T. D.; Haywood, N.; Teixeira, A.; Hodges, G.; Barrett, E. L.; Miller, 
M. A. Partitioning into Phosphatidylcholine–Cholesterol Membranes: Liposome 
Measurements, Coarse-Grained Simulations, and Implications for Bioaccumulation. 
Environmental Science: Processes & Impacts, 2023, 25, 1082–1093. 
https://doi.org/10.1039/d3em00081h.

Potter, T. D.; Barrett, E. L.; Miller, M. A. Automated Coarse-Grained Mapping 
Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning. 
Journal of Chemical Theory and Computation, 2021, 17, 5777–5791. 
https://doi.org/10.1021/acs.jctc.1c00322.

Please cite these works if you use this code in your research. We thank Mark. A. Miller and coworkers for their contributions.

License

This software is distributed under the MIT license.

Copyright (c) 2024 Lorenz Friedrich Dettmann

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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