/SI-Excluded-Volume-Formation

SI for the article named "Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects"

Primary LanguageJupyter NotebookCreative Commons Attribution 4.0 InternationalCC-BY-4.0

DOI

Electronic notebook: Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects (GAFF/SPCE/Heyda force field)

This is supporting information for the scientific manuscript by Hervø-Hansen et al. (Chem. Sci., 2023, doi: 10.1039/D3SC04617F) on the solvation free energy of alcohols and alkanes in various electrolyte 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). For running the simulation we recommend you clone the repository.

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 gromacs format) for the various chemical species utilized.
  • Figures Directory containing publication ready figures and images imported in the Juypter notebooks.
  • Data Directory containing processed data such as Setschenow coefficients along with its species and energetic decompositions, and RDFs.
  • Forcefield_generation.ipynb Jupyter notebook for generating force field files in any format for arbitary molecules.
  • Simulations.ipynb Jupyter notebook for running molecular dynamics simulations using OpenMM.
  • Analysis.ipynb Jupyter notebook for analysis of simulations and production of publication ready figures.
  • environment.yml Conda environment file to recreate the simulation environment. The environment most importantly contains Numpy, Scipy, OpenMM, OpenMMTools, 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 CavityFormation
   jupyter-notebook

License

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

CC BY 4.0