Clean up rogue cell and reduce simulation times on Colab

openforcefield · Feb 27, 2024 · 4cf9d1e · 4cf9d1e
1 parent cefd7f2
commit 4cf9d1e
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 49 deletions.
diff --git a/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip b/source/workshops/2024/protein_prep/2024_protein_prep_workshop_materials.zip
diff --git a/source/workshops/2024/protein_prep/colab-protein_prep.ipynb b/source/workshops/2024/protein_prep/colab-protein_prep.ipynb
@@ -1083,7 +1083,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.step(100 * openmm.unit.picosecond / simulation.integrator.getStepSize())"
+    "simulation.step(1 * openmm.unit.picosecond / simulation.integrator.getStepSize())"
    ]
   },
   {
@@ -1119,7 +1119,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "simulation.step(100 * openmm.unit.picosecond / simulation.integrator.getStepSize())"
+    "simulation.step(1 * openmm.unit.picosecond / simulation.integrator.getStepSize())"
    ]
   },
   {
@@ -1171,19 +1171,19 @@
     "    openmm.app.XTCReporter(  # Compressed trajectory format\n",
     "        file=\"trajectory.xtc\",\n",
     "        reportInterval=int(\n",
-    "            1 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
+    "            0.01 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
     "        ),\n",
     "    ),\n",
     "    openmm.app.CheckpointReporter(  # Checkpoint for exact continuation in case of crash\n",
     "        file=\"checkpoint.chk\",\n",
     "        reportInterval=int(\n",
-    "            100 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
+    "            1 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
     "        ),\n",
     "    ),\n",
     "    openmm.app.StateDataReporter(  # Human readable state information over time\n",
     "        file=\"states.csv\",\n",
     "        reportInterval=int(\n",
-    "            1 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
+    "            0.01 * openmm.unit.picosecond / simulation.integrator.getStepSize()\n",
     "        ),\n",
     "        step=True,\n",
     "        time=True,\n",
@@ -1216,50 +1216,6 @@
     "simulation.runForClockTime(1 * openmm.unit.minute)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e8e54de6-f0af-413d-a119-2987daa36097",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def nglview_show_openmm(topology: openmm.app.Topology, positions, image_molecules=False):\n",
-    "    import mdtraj\n",
-    "    import openmm.unit\n",
-    "    import nglview\n",
-    "    \n",
-    "    top = mdtraj.Topology.from_openmm(topology)\n",
-    "\n",
-    "    if isinstance(positions, str) or isinstance(positions, Path):\n",
-    "        traj = mdtraj.load(positions, top=top)\n",
-    "        if image_molecules:\n",
-    "            traj.image_molecules(inplace=True)\n",
-    "    else:\n",
-    "        positions = ensure_quantity(positions, \"openmm\").value_in_unit(\n",
-    "            openmm.unit.nanometer\n",
-    "        )\n",
-    "        xyz = numpy.asarray([positions])\n",
-    "        box_vectors = topology.getPeriodicBoxVectors()\n",
-    "        if box_vectors is not None:\n",
-    "            (\n",
-    "                l1,\n",
-    "                l2,\n",
-    "                l3,\n",
-    "                alpha,\n",
-    "                beta,\n",
-    "                gamma,\n",
-    "            ) = mdtraj.utils.box_vectors_to_lengths_and_angles(\n",
-    "                *numpy.asarray(box_vectors.value_in_unit(openmm.unit.nanometer))\n",
-    "            )\n",
-    "            unitcell_angles, unitcell_lengths = [alpha, beta, gamma], [l1, l2, l3]\n",
-    "        else:\n",
-    "            unitcell_angles, unitcell_lengths = None, None\n",
-    "        traj = mdtraj.Trajectory(\n",
-    "            xyz, top, unitcell_lengths=unitcell_lengths, unitcell_angles=unitcell_angles\n",
-    "        )\n",
-    "    return nglview.show_mdtraj(traj)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "77f0ff3b-3ce3-4aa1-a77e-29b8582dc78a",