pl-validation

Verifying that persistence length calculations of conjugated donor acceptor polymers using flowermd are independent of each other.
This repository is based on work completed by Dr. Paul found here: https://github.com/cmelab/forcefields/tree/main
Polymers being studied (Danielsen et al.): https://pubs.acs.org/doi/10.1021/acs.macromol.1c02229#_i2

The ff_generation.ipynb generates mbuild monomers and their forcefields using ESPALOMA. A foyer forcefield is output that should work with an uncharged mol2 file.

poly_builder.ipynb uses mbuild to polymerize the monomers.

poly_min_working_example.ipynb contains code to run NVT shrinks and simulations.

data_analysis.ipynb has the requisite functions for calculating the persistence length of mbuild polymers.

To install environment:

git clone https://github.com/cmelab/pl-validation.git
conda env create -f environment.yml
conda activate p_l

Eric's notes:

ff_generation builds