reeds_protonation_tautomers

Description

This directory contains the analysis scripts and data (e.g. to reproduce figures) for the article (https://pubs.acs.org/doi/full/10.1021/acs.jctc.4c00370)

Input files to reproduce the RE-EDS simulations shown in this work are given in: input_files

The jupyter notebooks to reproduce the figures in the manuscript can be found in: paper_programs/notebooks

Installation

The analysis scripts are all written in Python. A conda environment file is provided with reeds_environment.yml. To install the environment, run the following command in the terminal:

mamba env create -f reeds_environment.yml

Additionally, the code relies on a few functions from the ''reeds pipeline'' which can be downloaded from:

git clone --recurse-submodules https://github.com/rinikerlab/reeds.git
export PYTHONPATH=$PYTHONPATH:/path/to/reeds

This will create a conda environment called reeds_tautomers. To activate the environment, run:

conda activate reeds_tautomers