Assorted cleanup and installation standardization

charmm-gui-gmx/charmm-gui-gmx.ipynb

@@ -31,13 +31,36 @@
     "while the MOL2 file serves as a prototype for constructing an `mb.Compound`"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Install requirements"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import mbuild as mb"
+    "!conda install --file requirements.txt --yes"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If `gmx` (the `GROMACS` executable) is not found, install it via `conda`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!if ! [ -x \"$(command -v gmx)\" ]; then conda install -c bioconda gromacs; fi"
    ]
   },
   {
@@ -56,6 +79,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import mbuild as mb\n",
+    "\n",
     "class charmm_ethane(mb.Compound):\n",
     "    def __init__(self):\n",
     "        super(charmm_ethane, self).__init__()\n",
@@ -257,7 +282,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,

charmm-gui-gmx/requirements.txt

@@ -0,0 +1,3 @@
+mbuild
+mdtraj
+matplotlib

smirnoff_omm/requirements.txt

@@ -0,0 +1,6 @@
+mbuild
+foyer
+parmed
+openforcefield<0.6
+openmm
+mdtraj