Set box vectors for GROMACS example

openforcefield · Nov 4, 2024 · e211978 · e211978
1 parent cec2532
commit e211978
Showing 1 changed file with 22 additions and 20 deletions.
diff --git a/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb b/examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb
@@ -40,7 +40,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from openff.toolkit import ForceField, Molecule, Topology"
+    "from openff.toolkit import ForceField, Molecule, Quantity, Topology"
    ]
   },
   {
@@ -74,10 +74,22 @@
     "tags": []
    },
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Support for writing out LAMMPS data files will be removed\n",
+      "in mbuild 1.0.\n",
+      "See GMSO (https://github.com/mosdef-hub/gmso/tree/main/gmso/formats/lammpsdata) for\n",
+      "continued support for LAMMPS.\n",
+      "\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "2f3b86c392c24705b86721395cf43ea4",
+       "model_id": "3ead8bf62c2d49f1b6776a59e34a7a1d",
        "version_major": 2,
        "version_minor": 0
       },
@@ -90,8 +102,8 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/_experimental.py:35: UserWarning: Interchange object combination is experimental and likely to produce strange results. Any workflow using this method is not guaranteed to be suitable for production. Use with extreme caution and thoroughly validate results!\n",
-      "  return func(*args, **kwargs)\n"
+      "/Users/mattthompson/software/openff-interchange/openff/interchange/operations/_combine.py:52: InterchangeCombinationWarning: Interchange object combination is complex and likely to produce strange results outside of a limited set of use cases it has been tested in. Any workflow using this method is not guaranteed to be suitable for production or stable between versions. Use with extreme caution and thoroughly validate results!\n",
+      "  warnings.warn(\n"
      ]
     }
    ],
@@ -109,9 +121,8 @@
     "\n",
     "complex_system = receptor.combine(ligand)\n",
     "\n",
-    "# TODO\n",
-    "# complex.box = pdbfile box vectors ...\n",
-    "# complex.positions = np.vstack([receptor.positions, ligand.positions])"
+    "# Pseudo-vacuum\n",
+    "complex_system.box = Quantity([5, 5, 5], \"nanometer\")"
    ]
   },
   {
@@ -129,7 +140,7 @@
     {
      "data": {
       "text/plain": [
-       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x14380adf0> >"
+       "<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x3442730f0> >"
       ]
      },
      "execution_count": 5,
@@ -175,16 +186,7 @@
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/jeffreywagner/projects/OpenForceField/openff-interchange/openff/interchange/interop/gromacs/export/_export.py:48: UserWarning: WARNING: System defined with no box vectors, which GROMACS does not offically support in versions 2020 or newer (see https://gitlab.com/gromacs/gromacs/-/issues/3526). Setting box vectors to a 5  nm cube.\n",
-      "  self._write_gro(gro, decimal)\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "complex_system.to_gro(\"complex.gro\")\n",
     "complex_system.to_top(\"complex.top\")"
@@ -194,7 +196,7 @@
  "metadata": {
   "category": "force_field_interop",
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -208,7 +210,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.15"
   }
  },
  "nbformat": 4,