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Polyply

Polyply is a Python suite designed to facilitate the generation of input files and system coordinates for simulating (bio)macromolecules such as synthetic polymers or polysaccharides.

Input files can be generated either from user-specified building blocks or by using the polymers available in the library. The library currently includes polymer definitions for the GROMOS (2016H66 & 53A6), OPLS, Parmbsc1, and Martini (2 & 3) force-fields. Coordinates are generated by a multiscale random-walk protocol that is able to generate condensed-phase systems at a target density, as well as more heterogeneous systems such as aqueous two-phase systems. In addition, polyply allows you to tailor initial chain conformations by providing a build file — for example, the persistence length can be used to control the initial chain dimensions.

Where to start

Always verify your results and give appropriate credit to the developers of the force-field, molecule parameters, and this program.

Citation

If you use polyply in your work, please cite:

@article{Grunewald2022Polyply,
  title={Polyply; a python suite for facilitating simulations of (bio-) macromolecules and nanomaterials},
  author={Gr{\"u}newald, Fabian and Alessandri, Riccardo and Kroon, Peter C and
          Monticelli, Luca and Souza, Paulo CT and Marrink, Siewert J},
  journal={Nature Communications},
  volume={13},
  pages={68},
  doi={https://doi.org/10.1038/s41467-021-27627-4},
  year={2022}
}

More details on the algorithm and its verification can be found in the publication.

Contributions & support

We are happy to accept submissions of polymer parameters to the polyply library — see Submit Polymer Parameters. Code development happens on GitHub; contributions are welcome as bug reports and pull requests. You can also reach out on the discussions board.

License

Polyply is distributed under the Apache 2.0 license. Copyright 2020 University of Groningen.