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OpenFE Notebooks

Collection of notebooks for the Open FreeEnergy project. These can be ran in the browser via the Binder links.

Binder link Description
Binder Showcase of the OpenFE package as a whole
Binder Demonstrating how to plan a free energy network and apply a protocol

Running these notebooks locally

To run these notebooks locally you will need to install the openfe package, this is best done using miniconda

Once miniconda is installed, from a terminal run:

  • conda create -n openfe -c conda-forge openfe jupyter
  • conda activate openfe

Then you can download a copy of the notebooks:

Or via the command line as:

  • wget https://github.com/OpenFreeEnergy/ExampleNotebooks/archive/refs/tags/nov-2022.tar.gz
  • tar xf nov-2022.tar.gz

Then navigate to the downloaded notebooks:

  • cd ExampleNotebooks-nov-2022/openmm-rbfe

Then launch the notebook application as:

  • jupyter notebook

This should present a choice of two notebooks to follow.