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update tutorials page

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2023-05-06 18:57:44 +01:00
committed by Richard Gowers
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docs/tutorials/index.rst
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Tutorials
=========
Soon we should make sure we can inline the tutorials. Until then, here are
some links:
.. todo: make sure we can inline the tutorial, for now we only provide links
OpenFE has several tutorial notebooks which are maintained on our
`Example Notebooks repository <https://github.com/OpenFreeEnergy/ExampleNotebooks>__`.
For new users, we recommend the following two:
Relative Free Energies CLI tutorial
-----------------------------------
The `Relative Free Energies with the OpenFE CLI <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/easy_campaign/cli-tutorial.md>__`
tutorial walks users through how to use the OpenFE command line to calculate
relative hydration free energies from a small set of benzene modifications.
Associated with it is also a `notebook <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/easy_campaign/rhfe-python-tutorial.ipynb>__`
for how to achieve the same outcomes using the Python API.
Python API Showcase
-------------------
Our `showcase notebook <https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb>__`
walks users through how to use the main components of OpenFE to create a
relative binding free energy calculation.
* CLI (could do with some explanation): https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/master/easyCampaign/OpenFE_run_easy_rbfe.sh
* Python API: https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/master/openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb