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Drude.ipynb

@@ -4,9 +4,7 @@
   "metadata": {
     "accelerator": "GPU",
     "colab": {
-      "name": "Drude.ipynb",
       "provenance": [],
-      "collapsed_sections": [],
       "include_colab_link": true
     },
     "kernelspec": {
@@ -166,13 +164,12 @@
         "!wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 2>&1 1>/dev/null\n",
         "!bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n",
         "!rm Miniconda3-latest-Linux-x86_64.sh\n",
-        "!conda install -y -q -c conda-forge openmm=7.6 python=3.7 pdbfixer 2>&1 1>/dev/null\n",
-        "!conda install -c ambermd pytraj  --yes 2>&1 1>/dev/null\n",
-        "\n",
+        "!conda install -y -q -c conda-forge openmm=7.6 python=3.8 pdbfixer 2>&1 1>/dev/null\n",
+        "!conda install -c conda-forge ambertools --yes 2>&1 1>/dev/null\n",
         "\n",
         "#load python libraries\n",
         "import sys\n",
-        "sys.path.append('/usr/local/lib/python3.7/site-packages/')\n",
+        "sys.path.append('/usr/local/lib/python3.8/site-packages/')\n",
         "from biopandas.pdb import PandasPdb\n",
         "import openmm as mm\n",
         "from openmm import *\n",
@@ -195,10 +192,7 @@
         "from statistics import mean, stdev\n",
         "from pytraj import matrix\n",
         "from matplotlib import colors\n",
-        "from IPython.display import set_matplotlib_formats\n",
-        "# %matplotlib inline\n",
-        "# set_matplotlib_formats('png')\n",
-        "# plt.figure(figsize=(5,7))"
+        "from IPython.display import set_matplotlib_formats"
       ],
       "execution_count": null,
       "outputs": []