diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5d36ed1..d881c9d 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -64,4 +64,4 @@ jobs:
 
     - name: Run example notebooks
       run: |
-        python -m pytest -v --nbval-lax --nbval-cell-timeout=3000 -n auto --dist loadscope
+        python -m pytest -v --nbval-lax --nbval-cell-timeout=6000 -n auto --dist loadscope
diff --git a/.gitignore b/.gitignore
index 6e57a5b..651d7bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -266,6 +266,7 @@ showcase/tyk2_edge.png
 showcase/tyk2_json/
 simulation_visualization/openfe_analysis_skipped/
 simulation_visualization/septop_structural_results/
+simulation_visualization/output
 execution/task*.db
 execution/warehouse*
 execution/mcl1_result_jsons/
diff --git a/simulation_visualization/simulation_visualization.ipynb b/simulation_visualization/simulation_visualization.ipynb
index dd0c69d..24d26d2 100644
--- a/simulation_visualization/simulation_visualization.ipynb
+++ b/simulation_visualization/simulation_visualization.ipynb
@@ -828,7 +828,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 30,
+   "id": "56d70f17-12ed-4983-b2ce-eb24c65ff264",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "out_dir = pathlib.Path(\"output\")\n",
+    "out_dir.mkdir(exist_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
    "id": "a276e16f-3266-41ce-bde2-ece0144fe24a",
    "metadata": {},
    "outputs": [
@@ -843,8 +854,8 @@
    ],
    "source": [
     "# Ligand A\n",
-    "state_a.write(\"septop_state_a_topology.pdb\")\n",
-    "with mda.Writer(\"septop_out_A.xtc\", n_atoms=len(state_a.atoms)) as w:\n",
+    "state_a.write(out_dir/\"septop_state_a_topology.pdb\")\n",
+    "with mda.Writer(str(out_dir/\"septop_out_A.xtc\"), n_atoms=len(state_a.atoms)) as w:\n",
     "    for ts in u_septop_0.trajectory:\n",
     "        w.write(state_a)"
    ]
@@ -859,11 +870,19 @@
     "# State B: protein + ligand B\n",
     "state_b = u_septop_1.select_atoms(\"protein\") + lig_B_1\n",
     "\n",
-    "state_b.write(\"septop_state_b_topology.pdb\")\n",
-    "with mda.Writer(\"septop_out_B.xtc\", n_atoms=len(state_b.atoms)) as w:\n",
+    "state_b.write(out_dir/\"septop_state_b_topology.pdb\")\n",
+    "with mda.Writer(str(out_dir/\"septop_out_B.xtc\"), n_atoms=len(state_b.atoms)) as w:\n",
     "    for ts in u_septop_1.trajectory:\n",
     "        w.write(state_b)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9ad77aaf-5c6b-4123-bf25-5553eb5977d0",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -882,7 +901,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.13"
+   "version": "3.13.16"
   }
  },
  "nbformat": 4,