small fixes

openmm_md/plain_md.ipynb

@@ -154,7 +154,7 @@
     "settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond # setting the nvt equilibration length to 10 ps\n",
     "settings.simulation_settings.equilibration_length = 0.01 * unit.nanosecond # setting the npt equilibration length to 10 ps\n",
     "settings.simulation_settings.production_length = 0.01 * unit.nanosecond # setting the npt production length to 10 ps\n",
-    "settings.engine_settings.compute_platform = 'CPU'"
+    "settings.engine_settings.compute_platform = 'CPU' # running the simulation on the cpu"
    ]
   },
   {
@@ -248,7 +248,7 @@
    "metadata": {},
    "source": [
     "## 4. Creating the `NonTransformation`\n",
-    "Once we have the `ChemicalSystem`s, and the `Protocol`, we can create the `NonTransformation`. "
+    "Once we have the `ChemicalSystem`s, and the `Protocol`, we can create the `NonTransformation`. `NonTransformation` here simply means that the system is not \"transformed\" between two end states as is the case in binding free energy calculations."
    ]
   },
   {
@@ -299,11 +299,11 @@
    "source": [
     "import pathlib\n",
     "# first we create the directory\n",
-    "transformation_dir = pathlib.Path(\"md_input\")\n",
-    "transformation_dir.mkdir(exist_ok=True)\n",
+    "md_dir = pathlib.Path(\"md_input\")\n",
+    "md_dir.mkdir(exist_ok=True)\n",
     "\n",
     "# then we write out the transformation\n",
-    "nontransformation.dump(transformation_dir / f\"{nontransformation.name}.json\")"
+    "nontransformation.dump(md_dir / f\"{nontransformation.name}.json\")"
    ]
   },
   {
@@ -317,10 +317,10 @@
     "stored. For example,\n",
     "\n",
     "```bash\n",
-    "openfe quickrun path/to/transformation.json -o results.json -d working-directory\n",
+    "openfe quickrun path/to/nontransformation.json -o results.json -d working-directory\n",
     "```\n",
     "\n",
-    "where `path/to/transformation.json` is the path to one of the files created above (`md_input/benzene_t4-lysozyme.json`).\n",
+    "where `path/to/nontransformation.json` is the path to one of the files created above (`md_input/benzene_t4-lysozyme.json`).\n",
     "\n",
     "**(b) Using the Python API**\n",
     "\n",