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MDAnalysis · Nov 29, 2024 · 963ef4c · 963ef4c
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,10 +2,9 @@
   "build": { "dockerfile": "Dockerfile" },
   "customizations": {
     "vscode": {
-      "extensions": ["ms-python.python", "ms-toolsai.jupyter"],
+      "extensions": ["ms-python.python", "ms-toolsai.jupyter", "donjayamanne.vscode-default-python-kernel"],
       "settings": {
-        "python.defaultInterpreterPath": "/opt/conda/envs/workshop/bin/python",
-        "jupyter.defaultKernel": "workshop"
+        "python.defaultInterpreterPath": "/opt/conda/envs/workshop/bin/python"
       }
     }
   },

diff --git a/activity/activity.ipynb b/activity/activity.ipynb
@@ -51,36 +51,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "ConnectionError",
-     "evalue": "IMDClient: No handshake packet received",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mTimeoutError\u001b[0m                              Traceback (most recent call last)",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/utils.py:89\u001b[0m, in \u001b[0;36mread_into_buf\u001b[0;34m(sock, buf)\u001b[0m\n\u001b[1;32m     88\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 89\u001b[0m     received \u001b[38;5;241m=\u001b[39m sock\u001b[38;5;241m.\u001b[39mrecv_into(view[total_received:])\n\u001b[1;32m     90\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m received \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n",
-      "\u001b[0;31mTimeoutError\u001b[0m: timed out",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001b[0;31mTimeoutError\u001b[0m                              Traceback (most recent call last)",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/IMDClient.py:226\u001b[0m, in \u001b[0;36mIMDClient._await_IMD_handshake\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    225\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 226\u001b[0m     read_into_buf(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_conn, h_buf)\n\u001b[1;32m    227\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\u001b[38;5;167;01mConnectionError\u001b[39;00m, \u001b[38;5;167;01mTimeoutError\u001b[39;00m, \u001b[38;5;167;01mException\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m e:\n",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/utils.py:97\u001b[0m, in \u001b[0;36mread_into_buf\u001b[0;34m(sock, buf)\u001b[0m\n\u001b[1;32m     96\u001b[0m     logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mread_into_buf excepting due to read timeout\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m---> 97\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m\n\u001b[1;32m     98\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBlockingIOError\u001b[39;00m:\n",
-      "\u001b[0;31mTimeoutError\u001b[0m: ",
-      "\nDuring handling of the above exception, another exception occurred:\n",
-      "\u001b[0;31mConnectionError\u001b[0m                           Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[2], line 4\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mimdclient\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mIMD\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m IMDReader\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mMDAnalysis\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m \u001b[38;5;21;01mmda\u001b[39;00m\n\u001b[0;32m----> 4\u001b[0m u \u001b[38;5;241m=\u001b[39m mda\u001b[38;5;241m.\u001b[39mUniverse(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msample_simulation/imdgroup.gro\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mimd://localhost:8889\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m      6\u001b[0m \u001b[38;5;66;03m# Get an atom from the topology\u001b[39;00m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;66;03m# Universe -> AtomGroup -> Atom\u001b[39;00m\n\u001b[1;32m      8\u001b[0m atom \u001b[38;5;241m=\u001b[39m u\u001b[38;5;241m.\u001b[39matoms[\u001b[38;5;241m0\u001b[39m]\n",
-      "File \u001b[0;32m~/anaconda3/envs/imdclient-test/lib/python3.12/site-packages/MDAnalysis/core/universe.py:375\u001b[0m, in \u001b[0;36mUniverse.__init__\u001b[0;34m(self, topology, all_coordinates, format, topology_format, transformations, guess_bonds, vdwradii, fudge_factor, lower_bound, in_memory, in_memory_step, *coordinates, **kwargs)\u001b[0m\n\u001b[1;32m    370\u001b[0m coordinates \u001b[38;5;241m=\u001b[39m _resolve_coordinates(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfilename, \u001b[38;5;241m*\u001b[39mcoordinates,\n\u001b[1;32m    371\u001b[0m                                    \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mformat\u001b[39m,\n\u001b[1;32m    372\u001b[0m                                    all_coordinates\u001b[38;5;241m=\u001b[39mall_coordinates)\n\u001b[1;32m    374\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m coordinates:\n\u001b[0;32m--> 375\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mload_new(coordinates, \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mformat\u001b[39m, in_memory\u001b[38;5;241m=\u001b[39min_memory,\n\u001b[1;32m    376\u001b[0m                 in_memory_step\u001b[38;5;241m=\u001b[39min_memory_step, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m    378\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m transformations:\n\u001b[1;32m    379\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mcallable\u001b[39m(transformations):\n",
-      "File \u001b[0;32m~/anaconda3/envs/imdclient-test/lib/python3.12/site-packages/MDAnalysis/core/universe.py:580\u001b[0m, in \u001b[0;36mUniverse.load_new\u001b[0;34m(self, filename, format, in_memory, in_memory_step, **kwargs)\u001b[0m\n\u001b[1;32m    577\u001b[0m \u001b[38;5;66;03m# supply number of atoms for readers that cannot do it for themselves\u001b[39;00m\n\u001b[1;32m    578\u001b[0m kwargs[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mn_atoms\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms\u001b[38;5;241m.\u001b[39mn_atoms\n\u001b[0;32m--> 580\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtrajectory \u001b[38;5;241m=\u001b[39m reader(filename, \u001b[38;5;28mformat\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mformat\u001b[39m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m    581\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtrajectory\u001b[38;5;241m.\u001b[39mn_atoms \u001b[38;5;241m!=\u001b[39m \u001b[38;5;28mlen\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39matoms):\n\u001b[1;32m    582\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mThe topology and \u001b[39m\u001b[38;5;132;01m{form}\u001b[39;00m\u001b[38;5;124m trajectory files don\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    583\u001b[0m                      \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m have the same number of atoms!\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m    584\u001b[0m                      \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTopology number of atoms \u001b[39m\u001b[38;5;132;01m{top_n_atoms}\u001b[39;00m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m   (...)\u001b[0m\n\u001b[1;32m    588\u001b[0m                          fname\u001b[38;5;241m=\u001b[39mfilename,\n\u001b[1;32m    589\u001b[0m                          trj_n_atoms\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtrajectory\u001b[38;5;241m.\u001b[39mn_atoms))\n",
-      "File \u001b[0;32m~/anaconda3/envs/imdclient-test/lib/python3.12/site-packages/MDAnalysis/lib/util.py:2553\u001b[0m, in \u001b[0;36mstore_init_arguments.<locals>.wrapper\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m   2551\u001b[0m             \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m   2552\u001b[0m                 \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_kwargs[key] \u001b[38;5;241m=\u001b[39m arg\n\u001b[0;32m-> 2553\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m func(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/IMD.py:62\u001b[0m, in \u001b[0;36mIMDReader.__init__\u001b[0;34m(self, filename, convert_units, n_atoms, **kwargs)\u001b[0m\n\u001b[1;32m     59\u001b[0m host, port \u001b[38;5;241m=\u001b[39m parse_host_port(filename)\n\u001b[1;32m     61\u001b[0m \u001b[38;5;66;03m# This starts the simulation\u001b[39;00m\n\u001b[0;32m---> 62\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_imdclient \u001b[38;5;241m=\u001b[39m IMDClient(host, port, n_atoms, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m     64\u001b[0m imdsinfo \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_imdclient\u001b[38;5;241m.\u001b[39mget_imdsessioninfo()\n\u001b[1;32m     65\u001b[0m \u001b[38;5;66;03m# NOTE: after testing phase, fail out on IMDv2\u001b[39;00m\n",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/IMDClient.py:65\u001b[0m, in \u001b[0;36mIMDClient.__init__\u001b[0;34m(self, host, port, n_atoms, socket_bufsize, multithreaded, **kwargs)\u001b[0m\n\u001b[1;32m     63\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_stopped \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m     64\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_conn \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_connect_to_server(host, port, socket_bufsize)\n\u001b[0;32m---> 65\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_imdsinfo \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_await_IMD_handshake()\n\u001b[1;32m     66\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_multithreaded \u001b[38;5;241m=\u001b[39m multithreaded\n\u001b[1;32m     68\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_multithreaded:\n",
-      "File \u001b[0;32m~/workspace/imdclient/imdclient/IMDClient.py:229\u001b[0m, in \u001b[0;36mIMDClient._await_IMD_handshake\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    227\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (\u001b[38;5;167;01mConnectionError\u001b[39;00m, \u001b[38;5;167;01mTimeoutError\u001b[39;00m, \u001b[38;5;167;01mException\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m    228\u001b[0m     logger\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIMDClient: No handshake packet received: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, e)\n\u001b[0;32m--> 229\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mConnectionError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIMDClient: No handshake packet received\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    231\u001b[0m header \u001b[38;5;241m=\u001b[39m IMDHeader(h_buf)\n\u001b[1;32m    233\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m header\u001b[38;5;241m.\u001b[39mtype \u001b[38;5;241m!=\u001b[39m IMDHeaderType\u001b[38;5;241m.\u001b[39mIMD_HANDSHAKE:\n",
-      "\u001b[0;31mConnectionError\u001b[0m: IMDClient: No handshake packet received"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
@@ -113,23 +86,7 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/law/anaconda3/envs/imdclient-test/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "At time 0.070 fs, the n-terminus and c-terminus are 20.697 angrstroms apart\r"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
@@ -151,35 +108,15 @@
    "metadata": {},
    "source": [
     "## Live visualization of an analysis\n",
-    "\n"
+    "\n",
+    "Finally, we'll use matplot to create a live visualization of the distance between the two atoms."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/law/anaconda3/envs/imdclient-test/lib/python3.12/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    },
-    {
-     "ename": "ValueError",
-     "evalue": "",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[1], line 22\u001b[0m\n\u001b[1;32m     19\u001b[0m nter \u001b[38;5;241m=\u001b[39m u\u001b[38;5;241m.\u001b[39mselect_atoms(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mresid 1 and name CA\u001b[39m\u001b[38;5;124m\"\u001b[39m)\u001b[38;5;241m.\u001b[39matoms[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m     20\u001b[0m cter \u001b[38;5;241m=\u001b[39m u\u001b[38;5;241m.\u001b[39mselect_atoms(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mresid 129 and name CA\u001b[39m\u001b[38;5;124m\"\u001b[39m)\u001b[38;5;241m.\u001b[39matoms[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m---> 22\u001b[0m graph \u001b[38;5;241m=\u001b[39m LiveScalarGraph(\n\u001b[1;32m     23\u001b[0m     time_window\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1.0\u001b[39m, \u001b[38;5;66;03m# ps\u001b[39;00m\n\u001b[1;32m     24\u001b[0m     dt\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0.010\u001b[39m, \u001b[38;5;66;03m# ps\u001b[39;00m\n\u001b[1;32m     25\u001b[0m     title\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDistance vs. Time\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     26\u001b[0m     ylabel\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mDistance (Å)\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     27\u001b[0m     legend_label\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mNter-Cter\u001b[39m\u001b[38;5;124m'\u001b[39m,\n\u001b[1;32m     28\u001b[0m )\n\u001b[1;32m     30\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m ts \u001b[38;5;129;01min\u001b[39;00m u\u001b[38;5;241m.\u001b[39mtrajectory:\n\u001b[1;32m     31\u001b[0m     distance \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39msqrt(np\u001b[38;5;241m.\u001b[39msum((nter\u001b[38;5;241m.\u001b[39mposition \u001b[38;5;241m-\u001b[39m cter\u001b[38;5;241m.\u001b[39mposition) \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39m \u001b[38;5;241m2\u001b[39m))\n",
-      "File \u001b[0;32m~/workspace/imd-workshop-2024/activity/graph_utils.py:9\u001b[0m, in \u001b[0;36mLiveScalarGraph.__init__\u001b[0;34m(self, time_window, dt, title, ylabel, legend_label)\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m__init__\u001b[39m(\u001b[38;5;28mself\u001b[39m, time_window, dt, title\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m, ylabel\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m, legend_label\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m      8\u001b[0m     plt\u001b[38;5;241m.\u001b[39mion()\n\u001b[0;32m----> 9\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m\n\u001b[1;32m     10\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtime_window \u001b[38;5;241m=\u001b[39m time_window\n\u001b[1;32m     11\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mn_times \u001b[38;5;241m=\u001b[39m (\u001b[38;5;28mint\u001b[39m)(time_window \u001b[38;5;241m/\u001b[39m dt)\n",
-      "\u001b[0;31mValueError\u001b[0m: "
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from imdclient.IMD import IMDReader\n",
     "import numpy as np\n",
@@ -205,6 +142,42 @@
     "\n",
     "\n"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Challenge 1\n",
+    "\n",
+    "Your first challenge is to implement a new analysis function that calculates the number of water molecules within 4 angstroms of the protein during each timestep.\n",
+    "\n",
+    "Bonus points if you can create a live visualization of this data!\n",
+    "\n",
+    "*Hint*: \n",
+    "\n",
+    "All water molecules in the simulation can be selected like this:\n",
+    "```python\n",
+    "u.select_atoms('resname SOL')\n",
+    "```\n",
+    "For more advanced selection tips, see the [MDAnalysis documentation](https://userguide.mdanalysis.org/stable/selections.html)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from imdclient.IMD import IMDReader\n",
+    "import numpy as np\n",
+    "import MDAnalysis as mda\n",
+    "from graph_utils import LiveTimeseriesGraph\n",
+    "\n",
+    "u = mda.Universe(\"sample_simulation/imdgroup.gro\", \"imd://localhost:8889\")\n",
+    "\n",
+    "for ts in u.trajectory:\n",
+    "    ## Your analysis code here"
+   ]
   }
  ],
  "metadata": {

diff --git a/activity/run.sh b/activity/run.sh
@@ -1,21 +1,5 @@
 #!/bin/bash
 
-## TMP
-source /usr/local/gromacs/bin/GMXRC
-
-## WAIT UNTIL PORT IS OPEN
-SECONDS=0
-while lsof -n -i :8889; do
-    echo "Waiting for port 8889 to open"
-    sleep 1
-
-    if [ $SECONDS -ge 30 ]; then
-        echo "Timeout reached. Port 8889 did not open."
-        exit 1
-    fi
-done
-
-mkdir -p sample_simulation
 cd sample_simulation
 
 ## RUN GROMPP