Topology files and Python tool for "Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules"
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2024
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| author | Dettmann, Lorenz F. Kühn, Oliver A. Ahmed, Ashour |
| author_facet | Dettmann, Lorenz F. Kühn, Oliver A. Ahmed, Ashour |
| contents | <p>Topology files and Python tool with which the simulations of the study “Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules” can be reproduced. An updated version of the tool is also available on GitHub: <a href="https://github.com/LorenzDettmann/SOM2CG">https://github.com/LorenzDettmann/SOM2CG</a></p> <p>The topology files from the previous study (Dettmann et al. 2024, DOI: 10.1021/acs.jctc.4c00332) can be used for the reparametrization. The “scg_optimize” command must then be supplemented by the flags “-max_fct_bonds_f1 12000” and “-max_fct_angles_f1 350”. The “reparametrization.zip” file contains the files for the spectra calculation and their results, except for the trajectory files and the general Martini topology files.</p> <p>“SOM_compositions.zip” contains all the topology files required for reproducing the SOM simulations and for the benchmark calculations. </p> <p>Please note that all simulations were carried out with the GROMACS software package version 2019.4. For GROMACS 2023 and later, the options <code>nsttcouple = 10</code> and <code>nstpcouple = 10</code> should be explicitly added to the <code>.mdp</code> files. You can also obtain updated versions of these files from the GitHub repository mentioned above. Test simulations with the GROMACS 2022 release series have led to crashes and are therefore not recommended for these models.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_12942690 |
| institution | Zenodo |
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| publishDate | 2024 |
| publisher | Zenodo |
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| spellingShingle | Topology files and Python tool for "Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules" Dettmann, Lorenz F. Kühn, Oliver A. Ahmed, Ashour <p>Topology files and Python tool with which the simulations of the study “Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules” can be reproduced. An updated version of the tool is also available on GitHub: <a href="https://github.com/LorenzDettmann/SOM2CG">https://github.com/LorenzDettmann/SOM2CG</a></p> <p>The topology files from the previous study (Dettmann et al. 2024, DOI: 10.1021/acs.jctc.4c00332) can be used for the reparametrization. The “scg_optimize” command must then be supplemented by the flags “-max_fct_bonds_f1 12000” and “-max_fct_angles_f1 350”. The “reparametrization.zip” file contains the files for the spectra calculation and their results, except for the trajectory files and the general Martini topology files.</p> <p>“SOM_compositions.zip” contains all the topology files required for reproducing the SOM simulations and for the benchmark calculations. </p> <p>Please note that all simulations were carried out with the GROMACS software package version 2019.4. For GROMACS 2023 and later, the options <code>nsttcouple = 10</code> and <code>nstpcouple = 10</code> should be explicitly added to the <code>.mdp</code> files. You can also obtain updated versions of these files from the GitHub repository mentioned above. Test simulations with the GROMACS 2022 release series have led to crashes and are therefore not recommended for these models.</p> |
| title | Topology files and Python tool for "Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules" |
| url | https://doi.org/10.5281/zenodo.12942690 |