Merge pull request #731 from OpenFreeEnergy/add_tutorial_md

Add an MD tutorial
OpenFreeEnergy · Mar 27, 2024 · 0ca84d3 · 0ca84d3
2 parents 1dd5d7e + 1e71f74
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diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
@@ -25,6 +25,12 @@ 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.
 
+Molecular Dynamics (MD) protocol tutorial
+-----------------------------------------
+
+The :any:`MD protocol <md_tutorial>`
+tutorial walks users through how to run an MD simulation of benzene bound to 
+T4-lysozyme L99A in OpenFE.
 
 .. toctree::
     :maxdepth: 1
@@ -33,3 +39,4 @@ relative binding free energy calculation.
     rbfe_cli_tutorial
     rbfe_python_tutorial
     showcase_notebook
+    md_tutorial
diff --git a/docs/tutorials/md_tutorial.nblink b/docs/tutorials/md_tutorial.nblink
@@ -0,0 +1,6 @@
+{
+   "path": "../ExampleNotebooks/openmm_md/plain_md.ipynb",
+   "extra-media": [
+      "../ExampleNotebooks/openmm_md/assets/"
+   ]
+}