OpenFreeEnergy / ExampleNotebooks

Notebooks demonstrating how to do simple tasks related to free energy calculations.

OpenFE Notebooks

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

Binder link	Description
	Start here. This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the openfe package.
	Demonstrating how to plan a free energy network and apply a protocol Note: This notebook might not load if Binder is experiencing heavy usage.

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 MDAnalysis nglview
• conda activate openfe

Then you can download a copy of the notebooks:

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

Or via the command line as:

• wget -O OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/master
• or (depending on your platform)
• curl -L -k -o OpenFEEXampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/master

Unpack, then navigate to the downloaded notebooks:

• tar -xz OpenFEExampleNotebooks.tar.gz
• cd OpenFreeEnergy-ExampleNotebooks-b79be48

Then launch the notebook application as:

• jupyter notebook

This should present a choice of notebooks to follow.