diff --git a/charmm-gui-gmx/charmm-gui-gmx.ipynb b/charmm-gui-gmx/charmm-gui-gmx.ipynb
index aee2bff..ff01c19 100644
--- a/charmm-gui-gmx/charmm-gui-gmx.ipynb
+++ b/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,
diff --git a/charmm-gui-gmx/requirements.txt b/charmm-gui-gmx/requirements.txt
new file mode 100644
index 0000000..cf75c3e
--- /dev/null
+++ b/charmm-gui-gmx/requirements.txt
@@ -0,0 +1,3 @@
+mbuild
+mdtraj
+matplotlib
diff --git a/smirnoff_omm/requirements.txt b/smirnoff_omm/requirements.txt
new file mode 100644
index 0000000..81bbbe2
--- /dev/null
+++ b/smirnoff_omm/requirements.txt
@@ -0,0 +1,6 @@
+mbuild
+foyer
+parmed
+openforcefield<0.6
+openmm
+mdtraj
diff --git a/smirnoff_omm/smirnoff.ipynb b/smirnoff_omm/smirnoff.ipynb
index e61f74f..fb47332 100644
--- a/smirnoff_omm/smirnoff.ipynb
+++ b/smirnoff_omm/smirnoff.ipynb
@@ -4,22 +4,34 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## You will need\n",
-    "Openforcefield\n",
-    "`conda install -c omnia openforcefield`\n",
-    "\n",
-    "Smirnoff FF\n",
-    "`conda install -c omnia smirnoff99frosst`\n",
-    "(You may also need to clone [the smirnoff repo](https://github.com/openforcefield/smirnoff99Frosst) and pip install it to get the setuptools entry points to work)\n",
-    "\n",
-    "Also: mbuild, foyer, parmed, openmm, mdtraj, nglview"
+    "## Install requirements"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!conda config --add channels omnia && \\\n",
+    "conda config --add channels mosdef && \\\n",
+    "conda config --add channels conda-forge"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!conda install --file requirements.txt --yes && conda install -c omnia smirnoff99frosst --yes"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Building the our molecular system and model\n",
+    "## Build the molecular system and model\n",
     "We begin with some imports. We can already see a variety of packages being used: mBuild, Foyer, ParmEd, OpenForceField, Simtk, OpenMM, MDTraj, and NGLView. \n",
     "\n",
     "Take note of all the different data structure interconversions happening. There are *a lot*. This is good that we can get these API working together this often, but maybe not-so-good that we have to do these interconversions so often\n",
@@ -29,43 +41,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "eb82828e746746eb939f798763e64d0c",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "_ColormakerRegistry()"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/ayang41/anaconda3/envs/mosdef37/lib/python3.7/site-packages/nglview/widget.py:162: DeprecationWarning: Traits should be given as instances, not types (for example, `Int()`, not `Int`). Passing types is deprecated in traitlets 4.1.\n",
-      "  _ngl_view_id = List(Unicode).tag(sync=True)\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# MoSDeF tools for initializing and parametrizing systems\n",
-    "import mbuild\n",
-    "from mbuild.examples import Ethane\n",
+    "import mbuild as mb\n",
     "import foyer\n",
     "\n",
     "# ParmEd for interconverting data structures\n",
@@ -86,43 +67,18 @@
    "metadata": {},
    "source": [
     "We will use mBuild to create a generic Ethane ($C_2H_6$) molecule. \n",
-    "While this is imported from the examples, mBuild functionality allows users to construct chemical systems in a lego-like fashion by declaring particles and bonding them. \n",
+    "While this is imported from Open Babel via a SMILES string, mBuild functionality allows users to construct chemical systems in a lego-like fashion by declaring particles and bonding them. \n",
     "Under the hood, rigid transformations are performed to orient particles-to-be-bonded"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/ayang41/Programs/mbuild/mbuild/utils/io.py:120: DeprecationWarning: openbabel 2.0 detected and will be dropped in a future release. Consider upgrading to 3.x.\n",
-      "  warnings.warn(msg, DeprecationWarning)\n",
-      "/Users/ayang41/Programs/mbuild/mbuild/utils/io.py:120: DeprecationWarning: openbabel 2.0 detected and will be dropped in a future release. Consider upgrading to 3.x.\n",
-      "  warnings.warn(msg, DeprecationWarning)\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "939b956d2c20446ca4dd9922b5eb39e8",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "NGLWidget()"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "mbuild_compound = Ethane()\n",
-    "mbuild_compound.visualize(backend='nglview')"
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mbuild_compound = mb.load('CC', smiles=True)\n",
+    "mbuild_compound.visualize(backend='py3dmol')"
    ]
   },
   {
@@ -135,25 +91,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['CC\\tEthane\\n']\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/ayang41/Programs/mbuild/mbuild/utils/io.py:120: DeprecationWarning: openbabel 2.0 detected and will be dropped in a future release. Consider upgrading to 3.x.\n",
-      "  warnings.warn(msg, DeprecationWarning)\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "ethane_obmol = mbuild_compound.to_pybel()\n",
     "ethane_obmol.write(\"smi\", 'out.smi', overwrite=True)\n",
@@ -172,18 +112,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "<Topology; 1 chains, 1 residues, 8 atoms, 7 bonds>\n",
-      "[Vec3(x=2.819666989525475e-16, y=-1.4, z=-1.4644271506889933e-16), Vec3(x=-1.0699999332427972, y=-1.4000000000000001, z=-6.273541601638111e-17), Vec3(x=0.3570000827312472, y=-2.169000053405761, z=0.6530000269412993), Vec3(x=0.3570000827312474, y=-1.5810000836849212, z=-0.9929999709129338), Vec3(x=0.0, y=0.0, z=0.0), Vec3(x=1.0699999332427979, y=0.0, z=0.0), Vec3(x=-0.35700008273124695, y=0.7690000534057617, z=0.6530000269412994), Vec3(x=-0.35700008273124695, y=0.18100008368492126, z=-0.9929999709129333)] A\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "omm_topology, xyz = foyer.forcefield.generate_topology(mbuild_compound, residues='Ethane')\n",
     "print(omm_topology)\n",
@@ -201,20 +132,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Molecule with name '' and SMILES '[H][C]([H])([H])[C]([H])([H])[H]'"
-      ]
-     },
-     "execution_count": 10,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "ethane_molecule = Molecule.from_smiles(smiles_string[0].split()[0])\n",
     "ethane_molecule"
@@ -229,20 +149,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<openforcefield.topology.topology.Topology at 0x113ad0748>"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "off_topology = Topology.from_openmm(omm_topology, unique_molecules=[ethane_molecule])\n",
     "off_topology"
@@ -269,22 +178,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<openforcefield.typing.engines.smirnoff.forcefield.ForceField at 0x114dd72e8>"
-      ]
-     },
-     "execution_count": 12,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "#off_forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')\n",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "off_forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')\n",
     "off_forcefield = ForceField('smirnoff99Frosst-1.1.0.offxml')\n",
     "off_forcefield"
    ]
@@ -301,30 +199,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Warning: In AmberToolsToolkitwrapper.compute_partial_charges_am1bcc: Molecule '' has more than one conformer, but this function will only generate charges for the first one.\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "<simtk.openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x111a4fde0> >"
-      ]
-     },
-     "execution_count": 13,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "smirnoff_omm_system = off_forcefield.create_openmm_system(off_topology)\n",
-    "smirnoff_omm_system"
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "smirnoff_omm_system = off_forcefield.create_openmm_system(off_topology)"
    ]
   },
   {
@@ -337,7 +216,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -380,20 +259,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "Quantity(value=44.96860291382222, unit=kilocalorie/mole)"
-      ]
-     },
-     "execution_count": 15,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "new_vectors = [[10*unit.nanometer, 0*unit.nanometer, 0*unit.nanometer], \n",
     "               [0*unit.nanometer, 10*unit.nanometer, 0*unit.nanometer],\n",
@@ -414,20 +282,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "<Structure 8 atoms; 1 residues; 7 bonds; PBC (orthogonal); NOT parametrized>"
-      ]
-     },
-     "execution_count": 16,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "pmd_structure = parmed.openmm.load_topology(omm_topology, system=smirnoff_omm_system, xyz=xyz)\n",
     "pmd_structure"
@@ -451,30 +308,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/ayang41/Programs/foyer/foyer/validator.py:132: ValidationWarning: You have empty smart definition(s)\n",
-      "  warn(\"You have empty smart definition(s)\", ValidationWarning)\n",
-      "/Users/ayang41/Programs/foyer/foyer/forcefield.py:248: UserWarning: Parameters have not been assigned to all impropers. Total system impropers: 8, Parameterized impropers: 0. Note that if your system contains torsions of Ryckaert-Bellemans functional form, all of these torsions are processed as propers\n",
-      "  warnings.warn(msg)\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "Quantity(value=37.52734328319192, unit=kilocalorie/mole)"
-      ]
-     },
-     "execution_count": 17,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "foyer_ff = foyer.Forcefield(name='oplsaa')\n",
     "opls_pmd_structure = foyer_ff.apply(mbuild_compound)\n",
@@ -514,23 +350,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[<simtk.openmm.openmm.NonbondedForce; proxy of <Swig Object of type 'OpenMM::NonbondedForce *' at 0x116245960> >,\n",
-       " <simtk.openmm.openmm.PeriodicTorsionForce; proxy of <Swig Object of type 'OpenMM::PeriodicTorsionForce *' at 0x116245a50> >,\n",
-       " <simtk.openmm.openmm.HarmonicAngleForce; proxy of <Swig Object of type 'OpenMM::HarmonicAngleForce *' at 0x116245a80> >,\n",
-       " <simtk.openmm.openmm.HarmonicBondForce; proxy of <Swig Object of type 'OpenMM::HarmonicBondForce *' at 0x116245ab0> >]"
-      ]
-     },
-     "execution_count": 18,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "smirnoff_omm_system.getForces()"
    ]
@@ -545,24 +367,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "[<simtk.openmm.openmm.HarmonicBondForce; proxy of <Swig Object of type 'OpenMM::HarmonicBondForce *' at 0x116245930> >,\n",
-       " <simtk.openmm.openmm.HarmonicAngleForce; proxy of <Swig Object of type 'OpenMM::HarmonicAngleForce *' at 0x116245b40> >,\n",
-       " <simtk.openmm.openmm.RBTorsionForce; proxy of <Swig Object of type 'OpenMM::RBTorsionForce *' at 0x116245b70> >,\n",
-       " <simtk.openmm.openmm.NonbondedForce; proxy of <Swig Object of type 'OpenMM::NonbondedForce *' at 0x116245ba0> >,\n",
-       " <simtk.openmm.openmm.CMMotionRemover; proxy of <Swig Object of type 'OpenMM::CMMotionRemover *' at 0x116245bd0> >]"
-      ]
-     },
-     "execution_count": 19,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "opls_omm_system.getForces()"
    ]
@@ -589,40 +396,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[Quantity(value=-0.18, unit=elementary charge), Quantity(value=0.35000000000000003, unit=nanometer), Quantity(value=0.276144, unit=kilojoule/mole)]\n",
-      "[Quantity(value=-0.0941, unit=elementary charge), Quantity(value=0.3399669508423535, unit=nanometer), Quantity(value=0.4577296, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=-0.18, unit=elementary charge), Quantity(value=0.35000000000000003, unit=nanometer), Quantity(value=0.276144, unit=kilojoule/mole)]\n",
-      "[Quantity(value=-0.0941, unit=elementary charge), Quantity(value=0.3399669508423535, unit=nanometer), Quantity(value=0.4577296, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n",
-      "[Quantity(value=0.06, unit=elementary charge), Quantity(value=0.25, unit=nanometer), Quantity(value=0.12552, unit=kilojoule/mole)]\n",
-      "[Quantity(value=0.0317, unit=elementary charge), Quantity(value=0.2649532787749369, unit=nanometer), Quantity(value=0.06568879999999999, unit=kilojoule/mole)]\n",
-      "---\n"
-     ]
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "opls_omm_nonbond_force = opls_omm_system.getForce(3)\n",
     "smirnoff_omm_nonbond_force = smirnoff_omm_system.getForce(0)\n",
@@ -654,7 +430,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -674,7 +450,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -696,7 +472,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -714,7 +490,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -730,24 +506,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e9a89ab7cb8f453ea70be365b2f3e427",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "NGLWidget(max_frame=109)"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "traj = mdtraj.load('trajectory.dcd', top='first_frame.pdb')\n",
     "nglview.show_mdtraj(traj)"
@@ -770,7 +531,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,
diff --git a/water-box/requirements.txt b/water-box/requirements.txt
new file mode 100644
index 0000000..9e6993b
--- /dev/null
+++ b/water-box/requirements.txt
@@ -0,0 +1,6 @@
+jupyter
+numpy
+mbuild
+foyer
+mdtraj
+matplotlib
diff --git a/water-box/water-box.ipynb b/water-box/water-box.ipynb
index 6bacec0..44aa26d 100644
--- a/water-box/water-box.ipynb
+++ b/water-box/water-box.ipynb
@@ -1,13 +1,63 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Water box\n",
+    "\n",
+    "This workflow demonstrates how to use MoSDeF to prepare, run, and briefly analyze an MD simulation of water"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Install requirements"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!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"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "import mbuild as mb\n",
-    "from foyer import Forcefield"
+    "import mbuild\n",
+    "import foyer"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Preparing the system coordinates\n",
+    "\n",
+    "After importing our libraries, can load in a water molecule from disk. Then, the packing function `fill_box` calls `PACKMOL` under the hood to place copies of this molecule in a cubic box."
    ]
   },
   {
@@ -33,6 +83,15 @@
     ")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Applying the force field\n",
+    "\n",
+    "We use `Foyer` to load the SPC/E force field, in XML format, and apply it to our system."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -43,6 +102,13 @@
     "system = spce.apply(water_box.to_parmed(residues=['water']))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Finally, we save out two of the files we need to run a `GROMACS` simulation. The GRO file stores atomic coordinates and the TOP file stores force field information."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -53,6 +119,15 @@
     "system.save('system.top', combine='all')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Running the simulation\n",
+    "\n",
+    "We need to call `grompp` to prepare the simulation and then run it with `mdrun`"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -65,12 +140,23 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [],
    "source": [
     "!gmx mdrun -v -deffnm npt"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Analyzing the simulation\n",
+    "\n",
+    "Here we use `MDTraj` to load trajectory data from disk and make a quick plot of the density over time compared to reference data."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -80,7 +166,7 @@
     "import mdtraj as md\n",
     "import numpy as np\n",
     "\n",
-    "trj = md.load('nvt.xtc', top='system.gro')"
+    "trj = md.load('npt.xtc', top='system.gro')"
    ]
   },
   {
@@ -91,7 +177,7 @@
    "source": [
     "rho = md.density(trj)\n",
     "\n",
-    "t_ref, rho_ref = np.loadtxt('ref_data/rho.txt')"
+    "rho_ref = np.loadtxt('ref_data/rho.txt')"
    ]
   },
   {
@@ -109,8 +195,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "plt.plot(trj.time, rho, 'b-')\n",
-    "plt.plot(t_ref, rho_ref, 'k-')"
+    "fig, ax = plt.subplots()\n",
+    "\n",
+    "ax.plot(trj.time, rho, 'b-', label='Data')\n",
+    "ax.plot(rho_ref[:, 0], rho_ref[:, 1], 'k-', label='Reference')\n",
+    "ax.legend()\n",
+    "ax.set_xlabel('Simulation time, ps')\n",
+    "ax.set_ylabel('System density, kg/m^3')"
    ]
   }
  ],
@@ -130,7 +221,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.6"
   }
  },
  "nbformat": 4,