Add note about ASE units

IRL2 · Oct 11, 2024 · 9b5f879 · 9b5f879
1 parent 12097d7
commit 9b5f879
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/examples/ase/ase_openmm_nanotube.ipynb b/examples/ase/ase_openmm_nanotube.ipynb
@@ -198,7 +198,9 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": "As we are running the OpenMM simulation via ASE, we can use the ASE functionality to run a few simulation steps to check that everything is working:"
+   "source": [
+    "As we are running the OpenMM simulation via ASE, we can use the ASE functionality to run a few simulation steps to check that everything is working:"
+   ]
   },
   {
    "cell_type": "code",
@@ -248,7 +250,7 @@
     {
      "data": {
       "text/plain": [
-       "29.37619863848655"
+       "0.30069013433609304"
       ]
      },
      "execution_count": 7,
@@ -257,6 +259,7 @@
     }
    ],
    "source": [
+    "# Note that this is the energy in eV, not kJ mol-1 (the standard units of ASE are different to those of OpenMM and NanoVer)\n",
     "nanotube_simulation.dynamics.atoms.get_potential_energy()"
    ]
   },
@@ -324,7 +327,7 @@
     {
      "data": {
       "text/plain": [
-       "24.45851002327552"
+       "5.304255185770594"
       ]
      },
      "execution_count": 9,
@@ -390,7 +393,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "2039748b2f864b1f94024a907af8b5c1",
+       "model_id": "e73ec3466e28447fbacfb2117035b005",
        "version_major": 2,
        "version_minor": 0
       },