diff --git a/openmm_md/plain_md.ipynb b/openmm_md/plain_md.ipynb
index 5c7af2d..bd99f88 100644
--- a/openmm_md/plain_md.ipynb
+++ b/openmm_md/plain_md.ipynb
@@ -462,13 +462,14 @@
     "dag = protocol.create(stateA=system, stateB=system, mapping=None)\n",
     "workdir = pathlib.Path('./')\n",
     "# Running the MD simulations\n",
-    "dagres = gufe.protocols.execute_DAG(\n",
-    "    dag,\n",
-    "    shared_basedir=workdir,\n",
-    "    scratch_basedir=workdir,\n",
-    "    keep_shared=True, # set this to True to save the outputs\n",
-    "    n_retries=3\n",
-    ")"
+    "# uncomment to run the simulation\n",
+    "# dagres = gufe.protocols.execute_DAG(\n",
+    "#     dag,\n",
+    "#     shared_basedir=workdir,\n",
+    "#     scratch_basedir=workdir,\n",
+    "#     keep_shared=True, # set this to True to save the outputs\n",
+    "#     n_retries=3\n",
+    "# )"
    ]
   },
   {
@@ -494,7 +495,7 @@
     }
    ],
    "source": [
-    "!ls shared_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0/"
+    "# !ls shared_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0/"
    ]
   },
   {