Add .load() line for polyalanine simulation to fix DCD issue

IRL2 · Aug 29, 2024 · 4c45823 · 4c45823
1 parent 8432bcb
commit 4c45823
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/examples/openmm/openmm_polyalanine.ipynb b/examples/openmm/openmm_polyalanine.ipynb
@@ -239,7 +239,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Saving the trajectory can be done in the regular way for OpenMM simulations: by attaching a reporter. Here we attach a DCD reporter to save the trajectory in the DCD format every 500 frames."
+    "Saving the trajectory can be done in the regular way for OpenMM simulations: by attaching a reporter. Here we attach a DCD reporter to save the trajectory in the DCD format every 500 frames.\n",
+    "\n",
+    "**Note**: It is essential to load the simulation _before_ attaching a DCD reporter, using the `.load()` function."
    ]
   },
   {
@@ -248,6 +250,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# Load the simulation\n",
+    "polyalanine_simulation.load()\n",
+    "\n",
     "# Attach the DCD reporter\n",
     "dcd_reporter = app.DCDReporter('output.dcd', 500)\n",
     "polyalanine_simulation.simulation.reporters.append(dcd_reporter)\n",