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).
Python 3 with packages argparse, math, sys, numpy, MDAnalysis. The requirements can be found in requirements.txt.
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] \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] \
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.
This project is licensed under the MIT License - see the LICENSE file for details.
If the script or the model is helpful, please cite:
[1] Shrestha R, Alessandri R, Vögele M, Souza P, Marrink S-J, Monticelli L. Martini 3 coarse-grained models for carbon nanomaterials. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-6s1wj This content is a preprint and has not been peer-reviewed.