Workshop: timing fixed

Author: amruthesht

workshop/workshop.ipynb

@@ -30,13 +30,15 @@
     "\n",
     "| Time | Section | Topic |\n",
     "|------|---------|-------|\n",
-    "| 0-5 min | **Setup** | Connect to simulation |\n",
-    "| 5-15 min | **Application 1** | Continuous monitoring |\n",
-    "| 15-25 min | **Application 2** | Monitoring with breaks |\n",
-    "| 25-35 min | **Application 3** | Adaptive and selective sampling |\n",
-    "| 35-45 min | **Application 4** | Live visualization |\n",
-    "| 45-52 min | **Exercise 1** | Hydration shell analysis |\n",
-    "| 52-60 min | **Exercise 2** | Radius of gyration |\n",
+    "| 0-5 min | **Setup** | Workspace Codespace setup |\n",
+    "| 5-12 min | **Introduction** | Connecting to Simulation |\n",
+    "| 12-15 min | **Application 1** | Continuous monitoring |\n",
+    "| 15-24 min | **Application 2** | Monitoring with breaks |\n",
+    "| 24-29 min | **Application 3** | Adaptive and selective sampling |\n",
+    "| 29-35 min | **Application 4** | Live visualization |\n",
+    "| 35-47 min | **Exercise 1** | Charge Density Analysis |\n",
+    "| 47-59 min | **Exercise 2** | Root Mean Square Deviation (RMSD) |\n",
+    "| 59-60 min | **Wrap-up** | Q&A and next steps |\n",
     "\n",
     "Let's get started! 🚀"
    ]
@@ -110,6 +112,17 @@
     "print(f\"💧 Waters: {u.select_atoms('resname TIP3').n_residues} molecules\")\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Disconnect from the simulation\n",
+    "u.trajectory.close()\n",
+    "print(\"🔌 Disconnected from simulation.\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -138,7 +151,7 @@
     "### Step 4: Stopping and Restarting the Simulation\n",
     "\n",
     "**To stop the simulation:**\n",
-    "- In the terminal running `./run.sh`, press **Ctrl+C**\n",
+    "- In the terminal running `./run.sh`, press **Ctrl+C** (multiple times for certain Simulation Engines)\n",
     "- GROMACS will shut down gracefully\n",
     "\n",
     "**To restart:**\n",
@@ -429,6 +442,9 @@
     "\n",
     "# Create live plot\n",
     "plot = live_plot(title=\"Protein Radius of Gyration\", ylabel=\"Rg (Å)\", update_interval=1)\n",
+    "# Have fixed axis for better visualization\n",
+    "# plot[\"ax\"].set_xlim(0, 100)  # Time axis from 0 to 100 ps\n",
+    "# plot[\"ax\"].set_ylim(13, 16)   # Rg axis from 13 to 16 Å\n",
     "\n",
     "try:\n",
     "    for ts in u.trajectory:\n",
@@ -495,7 +511,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
     "import numpy as np\n",
     "from graph_utils import live_plot\n",
@@ -583,7 +598,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
     "from MDAnalysis.analysis import rms\n",
     "import numpy as np\n",