mlund / si-crownether-ion-binding

Counter Intuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites

Electronic Notebook: Counter Intuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites

Layout

• .zenodo.json This contains metedata for the Zenodo deposition. When you on github make a new Release, this can trigger a Zenodo build. To learn more about the available datafields, see here.
• README.md This is the file you're viewing right now. You may want to edit the Binder badge above to match your repository.
• environment.yml Defines the required Python packages using conda. It's a good idea to try to set specific versions of your dependencies as their behavior may change in the future. The environment is currently called my_environment and you'll likely want to rename it to something less generic.
• free_energy.py This contains the code used for generating the free energy landscape in the PCA analysis.
• notebook.ipynb This is the Jupyter Notebook, containing all the data analyses used for generating the published figures.

Requirements

To run the Notebooks online, click on the Launch Binder logo above. Alternatively, if you want to run on your own computer, install python using e.g. Miniconda or Anaconda) and make sure all required packages are loaded by issuing the following terminal commands

    conda env create -f environment.yml
    source activate bcetb
    jupyter-notebook