Add ASE functionality back into the nanotube notebook

examples/ase/ase_openmm_nanotube.ipynb

@@ -133,9 +133,11 @@
    ]
   },
   {
-   "metadata": {},
    "cell_type": "markdown",
-   "source": "Now we have our simulation ready, we can set up our NanoVer server to run the simulation. We run interactive ASE-OpenMM simulations in NanoVer using the `OmniRunner` class, which is in charge of serving and running the simulation."
+   "metadata": {},
+   "source": [
+    "Now we have our simulation ready, we can set up our NanoVer server to run the simulation. We run interactive ASE-OpenMM simulations in NanoVer using the `OmniRunner` class, which is in charge of serving and running the simulation."
+   ]
   },
   {
    "cell_type": "code",
@@ -171,7 +173,9 @@
     "    imd_runner.close()\n",
     "except NameError:\n",
     "    pass\n",
-    "imd_runner = OmniRunner.with_basic_server(nanotube_simulation, name=\"nanotube-ase-omm-server\")"
+    "imd_runner = OmniRunner.with_basic_server(nanotube_simulation, name=\"nanotube-ase-omm-server\")\n",
+    "imd_runner.next()\n",
+    "imd_runner.pause()"
    ]
   },
   {
@@ -194,17 +198,26 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "Let's get the simulation running"
-   ]
+   "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",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
-    "imd_runner.next()"
+    "nanotube_simulation.dynamics.run(10)"
    ]
   },
   {
@@ -215,7 +228,7 @@
     {
      "data": {
       "text/plain": [
-       "18"
+       "10"
       ]
      },
      "execution_count": 6,
@@ -235,7 +248,7 @@
     {
      "data": {
       "text/plain": [
-       "18.91275119857118"
+       "29.37619863848655"
       ]
      },
      "execution_count": 7,
@@ -275,6 +288,15 @@
   {
    "cell_type": "code",
    "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imd_runner.play()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2019-06-06T16:04:25.876184Z",
@@ -302,10 +324,10 @@
     {
      "data": {
       "text/plain": [
-       "33.20070838500853"
+       "24.45851002327552"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -362,13 +384,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d1de02c5fe4241ea9ff04bd6f6903a8a",
+       "model_id": "2039748b2f864b1f94024a907af8b5c1",
        "version_major": 2,
        "version_minor": 0
       },
@@ -441,7 +463,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -458,7 +480,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -467,7 +489,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -486,7 +508,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "metadata": {
     "ExecuteTime": {
      "end_time": "2019-06-06T16:04:26.778540Z",
@@ -505,7 +527,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -514,7 +536,7 @@
        "True"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -525,7 +547,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -534,7 +556,7 @@
        "True"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -559,7 +581,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [],
    "source": [