A Python-based toolkit that leverages the functionality of mBuild, part of the MoSDeF simulation suite, to create reproducible crosslinked polymer structures. The toolkit enables high control over the final structure, facilitating visualization and generation of molecular dynamics (MD) simulation inputs that are Transparent, Reproducible, Usable by Others, and Extensible (TRUE; DOI: https://doi.org/10.1080/00268976.2020.1742938).
To get started, first install the necessary packages to run the tutorials.
You can create the conda environment from the provided .yml file and then activate it:
conda env create -f conda_environment/original_env.yml -n Polylattice-MoSDeF
conda activate Polylattice-MoSDeFAfter creating the environment, go into the directory to install the dependencies:
cd Polylattice
python -m pip install -e .Once the environment and dependencies are ready, begin by exploring the Polymer_Chain_Creation.ipynb notebook to get familiarized with the MoSDeF–mBuild concepts behind the Polymer class and the subsequent creation of crosslinked polymer compounds.
This repository contains Examples for:
a) Polymer_Chain_Creation.ipynb: Building polymer compounds from custom repeat units
b) PVA.ipynb: PVA crosslinked with Glutaraldehyde, Dimethylolurea and Maleic Acid
c) BADGE_MHHPA.ipynb: Crosslinking of Bisphenol-A-diglycidyl-ether (BADGE:https://pubchem.ncbi.nlm.nih.gov/compound/Bisphenol-A-diglycidyl-ether) and crosslinker Methylhexahydrophthalic-anhydride (MHHPA: https://pubchem.ncbi.nlm.nih.gov/compound/Methylhexahydrophthalic-anhydride )
d) EPON-862_DETDA.ipynb: Crosslinking of a polyamide EPON 862 with the curing Agent DETDA (https://pubs.acs.org/doi/full/10.1021/ma2005519)
e) TETA-TMC*.ipynb: Crosslinking of a polyamide triethylentetramine (TETA) with trimesoyl chloride (TMC) (https://pubs.acs.org/doi/10.1021/acsomega.3c10108)
I) TETA_TMC_via_API.ipynb: Using PubChem's API for loading the initial monomers
II) TETA_TMC_via_MOL2.ipynb: Using mol2 files
f) PVA_Crosslinked_Uncrosslinked.ipynb: Creating a simulation box with a mixture of crosslinked and uncrosslinked PVA
To launch in Binder to visualize the output of the notebooks:
The examples shown in this repository are illustrative as the functionality of the code can be adapted to many other chemistries using the methodology and outlined strategies shown in the current repository.
If you use PolyLattice in your work, please cite: A. F. Ordorica, A. M. O. Mohamed, N. C. Craven, P. T. Cummings and C. McCabe, PolyLattice: A Reproducible Structure Generator for Crosslinked Polymers, RSC Adv., [year], [vol], [pages]. DOI: [DOI] Archived release: DOI 10.5281/zenodo.21443343