Electronic Notebook: Thermodynamics of Urea's Effects on the Solubility of Polyethylene Glycol

This is supporting information for the scientific manuscript by Hervø-Hansen et al. (J. Chem. Theory Comput., 2025, doi: 10.1021/acs.jctc.4c01000) on the solvation free energy of PEG in urea solutions using the energy-representation theory of solvation in combination with all-atom simulations. All figures within the analysis are publication ready and can be reproduced by running the provided Jupyter notebooks (.ipynb).

Layout

• PDB_files PDB files for various chemical species utilized.
• Simulations Directory containing raw ermod results and processed results. The directory is also used for location of trajectories and corresponding analysis upon reproduction.
• Force_fields Directory containing force parameters files (in OpenMM format) for the various chemical species utilized.
• Figures Directory containing publication ready figures and images imported in the Juypter notebooks.
• Data Directory containing pre-processed data.
• Simulations.ipynb Jupyter notebook for running molecular dynamics simulations using OpenMM.
• Analysis.ipynb Jupyter notebook for analysis of simulations and free energy computations and production of publication ready figures.
• ERmod.ipynb Jupyter notebook for running free energy calculations using energy-representation theory.
• environment.yml Conda environment file to recreate the simulation environment. The environment most importantly contains Numpy, Scipy, OpenMM, parmed, mdtraj, and Packmol.

Usage

To open the notebook, install Python via Miniconda and make sure all required packages are loaded by issuing the following terminal commands

   conda env create -f environment.yml
   conda activate PEO
   jupyter-notebook

License

This work is licensed under a Creative Commons Attribution 4.0 International License.