Martini 3 model of Graphene

Generates a Martini 3 model of both finite and infinite graphene sheet for running the molecular dynamics simulation with the Gromacs simulation package. The script outputs both the structure file (.gro) and a topology file (.itp).

Requirements

Python 3 with numpy and MDAnalysis. The runtime dependencies are listed in requirements.txt.

Usage

For generating the structure and topology of a finite graphene sheet, run

python Non-Periodic/martini3-graphene-topology.py -x [Length of the graphene sheet along x in nm] \
                                        -y [Length of the graphene sheet along y in nm] \
                                        -z [Length of the box along z in nm]
                                        -o [Name of the output for both structure and topology] \
                                        [--output-dir DIR] \
                                        [--force] \
                                        [--quiet] \
                                        [--profile] \

for example

python Non-Periodic/martini3-graphene-topology.py -x 21 -y 23 -z 30 -o graphene

All arguments are optional. If an argument is not used, the default value for their dimension (12 nm), and the name of the output (martini_graphene) is used.

Similarly, for generating the structure and topology of an infinite graphene sheet, run

python Periodic/martini3-graphene-periodic.py -x [Length of the graphene sheet along x in nm] \
                                     -y [Length of the graphene sheet along y in nm] \
                                     -z [Length of the box along z in nm]
                                     -o [Name of the output for both structure and topology] \
                                     [--output-dir DIR] \
                                     [--force] \
                                     [--quiet] \
                                     [--profile] \

for example

python Periodic/martini3-graphene-periodic.py -x 21 -y 23 -z 30 -o graphene

All arguments are optional. If an argument is not used, the default value for their dimension (12 nm), and the name of the output (martini_graphene) is used.

Both scripts also support:

• --output-dir DIR: write outputs to DIR.
• --force: overwrite existing output files (.gro and .itp) for the selected output name.
• --quiet: suppress non-essential stderr output.
• --profile: print stage timing information to stderr.

Without --force, the scripts stop if those output files already exist.

Example (overwrite existing files in a custom directory):

python Periodic/martini3-graphene-periodic.py -x 100 -y 100 -z 30 -o graphene --output-dir results --force

Graphitic Surface (Stacked Graphene)

To build a graphitic slab :

python graphite/build_graphite_slab.py -x 10 -y 10 --layers 5 -o graphite

This writes:

• graphene.gro, graphene.itp, graphene_1layer.gro
• graphite.gro, graphite.pdb
• posre_GRA.itp and appends a POSRES include block to graphene.itp
• topol.top with default Martini + graphene includes and GRA <layers>

See graphite/README.md for details.

Notes

• GRO atom indices are limited to 5 digits by the file format. For systems with more than 99,999 atoms, indices wrap around.
• The two generator scripts share internal utility code from graphene_shared.py.

Testing

Run the regression tests locally with:

python -m unittest discover -s tests -p "test_*.py" -v

The same test suite is run in GitHub Actions on pushes and pull requests.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use the script or the model, please cite:

Shrestha, R., Alessandri, R., Vögele, M., Hilpert, C., Souza, P. C. T., Marrink, S. J., & Monticelli, L. Martini 3 Coarse-Grained Models for Carbon Nanomaterials. J. Chem. Theory Comput., 2025, 21(18), 9035–9053. https://doi.org/10.1021/acs.jctc.5c00923

BibTeX

@article{Shrestha2025Martini3Carbon,
  author  = {Shrestha, Roshan and Alessandri, Riccardo and V{\"o}gele, Martin and Hilpert, C{\'e}cile and Souza, Paulo C. T. and Marrink, Siewert J. and Monticelli, Luca},
  title   = {Martini 3 Coarse-Grained Models for Carbon Nanomaterials},
  journal = {Journal of Chemical Theory and Computation},
  year    = {2025},
  volume  = {21},
  number  = {18},
  pages   = {9035--9053},
  doi     = {10.1021/acs.jctc.5c00923}
}