Add link to CLI tutorial

Author: hannahbaumann

openmm_rbfe/rbfe_membrane_protein.ipynb

@@ -1012,7 +1012,7 @@
    "source": [
     "## Writing the `Transformation`s to disk\n",
     "\n",
-    "We'll write out each transformation to disk, so that they can be run independently using the openfe quickrun command:"
+    "We'll write out each transformation to disk, so that they can be run independently using the `openfe quickrun` command:"
    ]
   },
   {
@@ -1031,6 +1031,14 @@
     "for transformation in network.edges:\n",
     "    transformation.to_json(transformation_dir / f\"{transformation.name}.json\")"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6f0085a5-d5a9-43b9-bb38-43deca490d2d",
+   "metadata": {},
+   "source": [
+    "Each of these individual `.json` files contains a `Transformation`, which contains all the information to run the calculation. These could be farmed out as individual jobs on a HPC cluster. For details on running them, please follow from the section on running simulations in the CLI tutorial (https://docs.openfree.energy/en/latest/tutorials/rbfe_cli_tutorial.html)"
+   ]
   }
  ],
  "metadata": {