https://github.com/mlund/si-crownether-ion-binding

Counter Intuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites
https://github.com/mlund/si-crownether-ion-binding

chemistry electrostatics molecular-dynamics reproducible-science theoretical-chemistry

Last synced: 11 months ago
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Counter Intuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites

• Host: GitHub
• URL: https://github.com/mlund/si-crownether-ion-binding
• Owner: mlund
• License: cc0-1.0
• Created: 2021-06-24T14:30:22.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2024-03-19T10:25:11.000Z (about 2 years ago)
• Last Synced: 2025-04-14T12:49:33.325Z (about 1 year ago)
• Topics: chemistry, electrostatics, molecular-dynamics, reproducible-science, theoretical-chemistry
• Language: Jupyter Notebook
• Homepage:
• Size: 40.4 MB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Zenodo: .zenodo.json

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README

          
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mlund/SI-crownether-ion-binding/main?filepath=notebook.ipynb)

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# 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](https://developers.zenodo.org/?python#depositions).

- `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](https://conda.io/miniconda.html) or [Anaconda](https://docs.conda.io))

and make sure all required packages are loaded by issuing the following terminal commands

``` bash

    conda env create -f environment.yml

    source activate bcetb

    jupyter-notebook

```