Merge pull request #201 from OpenFreeEnergy/update-md-tutorial

Update some settings in the MD tutorial to get outputs

Author: IAlibay

openmm_md/plain_md.ipynb

@@ -13,8 +13,7 @@
    "id": "7266db2c-37e5-419a-9015-929ea1635d98",
    "metadata": {},
    "source": [
-    "In this notebook we run an MD simulation of benzene bound to T4-lysozyme L99A.",
-    "![image](assets/t4lyso.png)"
+    "In this notebook we run an MD simulation of benzene bound to T4-lysozyme L99A.![image](assets/t4lyso.png)"
    ]
   },
   {
@@ -147,7 +146,9 @@
     "settings = PlainMDProtocol.default_settings()\n",
     "settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond # setting the nvt equilibration length to 10 ps\n",
     "settings.simulation_settings.equilibration_length = 0.01 * unit.nanosecond # setting the npt equilibration length to 10 ps\n",
-    "settings.simulation_settings.production_length = 0.01 * unit.nanosecond # setting the npt production length to 10 ps\n",
+    "# Setting the production length and checkpoint interval to 20 ps to match the trajectory write interval, so one frame will be written\n",
+    "settings.simulation_settings.production_length = 0.02 * unit.nanosecond # setting the npt production length to 20 ps\n",
+    "settings.output_settings.checkpoint_interval = 0.02 * unit.nanosecond # setting the checkpoint interval to 20 ps\n",
     "settings.engine_settings.compute_platform = 'CPU' # running the simulation on the cpu"
    ]
   },
@@ -161,7 +162,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'engine_settings': {'compute_platform': 'CPU'},\n",
+      "{'engine_settings': {'compute_platform': 'CPU', 'gpu_device_index': None},\n",
       " 'forcefield_settings': {'constraints': 'hbonds',\n",
       "                         'forcefields': ['amber/ff14SB.xml',\n",
       "                                         'amber/tip3p_standard.xml',\n",
@@ -171,15 +172,15 @@
       "                         'nonbonded_cutoff': <Quantity(1.0, 'nanometer')>,\n",
       "                         'nonbonded_method': 'PME',\n",
       "                         'rigid_water': True,\n",
-      "                         'small_molecule_forcefield': 'openff-2.0.0'},\n",
-      " 'integrator_settings': {'barostat_frequency': <Quantity(25, 'timestep')>,\n",
+      "                         'small_molecule_forcefield': 'openff-2.1.1'},\n",
+      " 'integrator_settings': {'barostat_frequency': <Quantity(25.0, 'timestep')>,\n",
       "                         'constraint_tolerance': 1e-06,\n",
       "                         'langevin_collision_rate': <Quantity(1.0, '1 / picosecond')>,\n",
       "                         'n_restart_attempts': 20,\n",
       "                         'reassign_velocities': False,\n",
       "                         'remove_com': False,\n",
-      "                         'timestep': <Quantity(4, 'femtosecond')>},\n",
-      " 'output_settings': {'checkpoint_interval': <Quantity(1, 'picosecond')>,\n",
+      "                         'timestep': <Quantity(4.0, 'femtosecond')>},\n",
+      " 'output_settings': {'checkpoint_interval': <Quantity(20.0, 'picosecond')>,\n",
       "                     'checkpoint_storage_filename': 'checkpoint.chk',\n",
       "                     'equil_npt_structure': 'equil_npt.pdb',\n",
       "                     'equil_nvt_structure': 'equil_nvt.pdb',\n",
@@ -189,7 +190,7 @@
       "                     'output_indices': 'not water',\n",
       "                     'preminimized_structure': 'system.pdb',\n",
       "                     'production_trajectory_filename': 'simulation.xtc',\n",
-      "                     'trajectory_write_interval': <Quantity(20, 'picosecond')>},\n",
+      "                     'trajectory_write_interval': <Quantity(20.0, 'picosecond')>},\n",
       " 'partial_charge_settings': {'nagl_model': None,\n",
       "                             'number_of_conformers': None,\n",
       "                             'off_toolkit_backend': 'ambertools',\n",
@@ -198,8 +199,12 @@
       " 'simulation_settings': {'equilibration_length': <Quantity(0.01, 'nanosecond')>,\n",
       "                         'equilibration_length_nvt': <Quantity(0.01, 'nanosecond')>,\n",
       "                         'minimization_steps': 5000,\n",
-      "                         'production_length': <Quantity(0.01, 'nanosecond')>},\n",
-      " 'solvation_settings': {'solvent_model': 'tip3p',\n",
+      "                         'production_length': <Quantity(0.02, 'nanosecond')>},\n",
+      " 'solvation_settings': {'box_shape': 'cube',\n",
+      "                        'box_size': None,\n",
+      "                        'box_vectors': None,\n",
+      "                        'number_of_solvent_molecules': None,\n",
+      "                        'solvent_model': 'tip3p',\n",
       "                        'solvent_padding': <Quantity(1.2, 'nanometer')>},\n",
       " 'thermo_settings': {'ph': None,\n",
       "                     'pressure': <Quantity(0.986923267, 'standard_atmosphere')>,\n",
@@ -286,7 +291,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "id": "7689c7ba-39a2-49ea-b82b-e3b198354c5b",
    "metadata": {},
    "outputs": [],
@@ -325,7 +330,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "544d037d-3a53-4390-91b8-3104c00694f0",
    "metadata": {
     "editable": true,
@@ -334,7 +339,17 @@
     },
     "tags": []
    },
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/hannahbaumann/miniforge3/envs/openfe_dev/lib/python3.12/site-packages/openfe/protocols/openmm_utils/omm_compute.py:76: UserWarning: Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n",
+      "  warnings.warn(wmsg)\n",
+      "WARNING:root:Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n"
+     ]
+    }
+   ],
    "source": [
     "import gufe\n",
     "import pathlib\n",
@@ -407,7 +422,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.12.8"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {