Merge branch 'main' into docs_protocol_cycles

docs/tutorials/ahfe_tutorial.nblink

@@ -0,0 +1,6 @@
+{
+   "path": "../ExampleNotebooks/ahfe_tutorial/python_tutorial.ipynb",
+   "extra-media": [
+      "../ExampleNotebooks/ahfe_tutorial/ahfe_cycle.png"
+   ]
+}

docs/tutorials/index.rst

@@ -5,11 +5,23 @@ Tutorials
 
 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:
 
+Here is a list of key tutorials which cover the different aspects of the
+OpenFE tooling:
+
+
+Relative Free Energies
+----------------------
+
+Python API Showcase
+~~~~~~~~~~~~~~~~~~~
+
+Our :any:`shocase notebook <showcase_notebook>` walks users through
+how to use the main Python API components of OpenFE to create a
+relative binding free energy calculation.
 
 Relative Free Energies CLI tutorial
------------------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The :any:`Relative Free Energies with the OpenFE CLI <rbfe_cli_tutorial>`
 tutorial walks users through how to use the OpenFE command line to calculate
@@ -18,12 +30,36 @@ relative binding free energies of various ligands against the TYK2 target.
 Associated with it is also a :any:`notebook <rbfe_python_tutorial>`
 for how to achieve the same outcomes using the Python API.
 
-Python API Showcase
--------------------
 
-Our :any:`showcase notebook <showcase_notebook>`
-walks users through how to use the main components of OpenFE to create a
-relative binding free energy calculation.
+Absolute Free Energies
+----------------------
+
+Absolute Solvation Free Energies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The :any:`Absolute Solvation Free Energy Protocol <ahfe_tutorial>` tutorial
+walks users through how to calculate the hydration free energy of a benzene
+ligand.
+
+
+Molecular Dynamics (MD)
+-----------------------
+
+The :any:`MD protocol <md_tutorial>`
+tutorial walks users through how to run a conventional (non-alchemical) MD
+simulation of benzene bound to T4-lysozyme L99A in OpenFE.
+
+
+Post Simulation Analysis
+------------------------
+
+Analyzing and Plotting RFE Networks with Cinnabar
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The :any:`Cinnabar tutorial <plotting_with_cinnabar>` demonstrates how to
+use the `Cinnabar Python package <https://github.com/OpenFreeEnergy/cinnabar>`_
+to analyze (e.g. generating MLE estimates of absolute free energies)
+and plot networks of relative free energy results.
 
 
 .. toctree::
@@ -33,3 +69,6 @@ relative binding free energy calculation.
     rbfe_cli_tutorial
     rbfe_python_tutorial
     showcase_notebook
+    md_tutorial
+    ahfe_tutorial
+    plotting_with_cinnabar

docs/tutorials/md_tutorial.nblink

@@ -0,0 +1,6 @@
+{
+   "path": "../ExampleNotebooks/openmm_md/plain_md.ipynb",
+   "extra-media": [
+      "../ExampleNotebooks/openmm_md/assets/"
+   ]
+}

docs/tutorials/plotting_with_cinnabar.nblink

@@ -0,0 +1,3 @@
+{
+   "path": "../ExampleNotebooks/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb"
+}