The Martini 3 Metabolome

Parameters, structure files, and parameterisation reference files for the Martini 3 Metabolome.

This repository is a subset of the full SI dataset available on Zenodo.

The currently available models are listed in the database.

If you are interested in using the parameters, the structure and parameter files are contained in the gros and itps subdirectories respectively.

If you are interested in more of the details of the parameterisation process, mapping files and figures comparing simulated and reference distributions are contained in the mappings and distributions subdirectories.

The misc folder contains any other files that may be relevant or of use. For the moment, it contains the database.md file in csv format, for ease of use.

Citation

If you use these parameters, please cite the relevant paper

@article {M3metabolites,
	author = {Brasnett, Christopher and Brown, Chelsea May and Gr{\"u}newald, Linus and Stevens, Jan A and Marrink, Siewert-Jan},
	title = {The Martini 3 Metabolome},
	year = {2026},
	doi = {10.64898/2026.03.06.710121},
	URL = {https://www.biorxiv.org/content/early/2026/03/09/2026.03.06.710121},
	journal = {bioRxiv}
}

Repo organisation

.
├── distributions
│   ├── nucleotide_plots
│   │   └── *.png
│   └── *.png
├── gros
│   └── *.gro
├── itps
│   ├── bonded
│   │   └── martini_v3.0.0_nucleotide_ffbonded_v1.itp
│   └── molecules
│       └── *.itp
├── mappings
│   ├── map_files
│   │       └── *.map
│   └── mappings.pdf
└── misc

Contributions

If there's a metabolite not covered by the parameters in the current set, we welcome all contributions subject to suitable validation. Contributions can be made through issues or pull requests. Please note that the decision of whether contributions can give authorship on the resulting academic paper is left to our sole discretion.

Full dataset

The full dataset (including reference atomistic trajectories) for the metabolome is available on Zenodo [LINK]