This package unites the many heuristic NP constructor methods and constructs bniomolecular and physical systems with the NPs, specifically with the Martini forcefield. The types of NPs supported with this package are:
- Ligand-functionalized NPs
- Carbon nanotubes
- Permutations of the C60 buckyball carbon nanoparticle
- Insertion into systems by leveraging the polyply program - https://github.com/marrink-lab/polyply_1.0
At the point of writing this (which is shown in the 'Last Updated' part of this documentation), the Ligand-functionalized part of this project is nearly complete, and the next step would be to integrate this with polyply. The way I am trying to add this project as a 'plugin' to that project is something I need to consider, and currently the main bottleneck I am facing.
Martini-PyNP requires:
- The Martini version of the NP builder can now account for building the itp file from ligand to NP.
- Integration with Martini Vermouth and polyply - the documentation on vermouth is scarce, meaning at the moment I have to look into the polyply code to see where exactly I can add this code as a 'plugin'.
- Python3
- NumPy
- simpletraj
- MDAnalysis
- rdkit
- parmed