Update mda_COG.ipynb

bjmorgan · Nov 16, 2023 · 3f201c5 · 3f201c5
1 parent a14d349
commit 3f201c5
Showing 1 changed file with 12 additions and 3 deletions.
diff --git a/docs/source/mda_COG.ipynb b/docs/source/mda_COG.ipynb
@@ -71,13 +71,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 18,
    "id": "61cc6b61-7e5b-4b87-ab8c-58ba55def62e",
    "metadata": {},
    "outputs": [],
    "source": [
-    "molecules = [[289,290,291,292,293,294],[285,296,297,298,299,300]]\n",
-    "masses    =  [12, 12, 1,  1,  1,  1]\n",
+    "molecules = [[289, 290, 291,   292,   293,   294],\n",
+    "             [285, 296, 297,   298,   299,   300]]\n",
+    "masses    =  [12,  12,  1.008, 1.008, 1.008, 1.008]\n",
     "\n",
     "p_parms = {'specie': None,\n",
     "           'time_step': 1.2e-03,\n",
@@ -88,6 +89,14 @@
     "           }"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "c9b5ea9a-2ba1-4d2b-8c27-e6a479721289",
+   "metadata": {},
+   "source": [
+    "With the parameters set, we now calcuate the mean squared-displacement."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 4,