Fix broken test

Author: hannahbaumann

cookbook/choose_protocol.ipynb

@@ -183,7 +183,7 @@
       "                         'softcore_alpha': 0.85,\n",
       "                         'turn_off_core_unique_exceptions': False,\n",
       "                         'use_dispersion_correction': False},\n",
-      " 'engine_settings': {'compute_platform': None},\n",
+      " 'engine_settings': {'compute_platform': None, 'gpu_device_index': None},\n",
       " 'forcefield_settings': {'constraints': 'hbonds',\n",
       "                         'forcefields': ['amber/ff14SB.xml',\n",
       "                                         'amber/tip3p_standard.xml',\n",
@@ -194,20 +194,22 @@
       "                         'nonbonded_method': 'PME',\n",
       "                         'rigid_water': True,\n",
       "                         'small_molecule_forcefield': 'openff-2.1.1'},\n",
-      " 'integrator_settings': {'barostat_frequency': <Quantity(25, 'timestep')>,\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",
+      "                         'timestep': <Quantity(4.0, 'femtosecond')>},\n",
       " 'lambda_settings': {'lambda_functions': 'default', 'lambda_windows': 11},\n",
-      " 'output_settings': {'checkpoint_interval': <Quantity(250, 'picosecond')>,\n",
+      " 'output_settings': {'checkpoint_interval': <Quantity(1.0, 'nanosecond')>,\n",
       "                     'checkpoint_storage_filename': 'checkpoint.chk',\n",
       "                     'forcefield_cache': 'db.json',\n",
       "                     'output_filename': 'simulation.nc',\n",
       "                     'output_indices': 'not water',\n",
-      "                     'output_structure': 'hybrid_system.pdb'},\n",
+      "                     'output_structure': 'hybrid_system.pdb',\n",
+      "                     'positions_write_frequency': <Quantity(100.0, 'picosecond')>,\n",
+      "                     'velocities_write_frequency': None},\n",
       " 'partial_charge_settings': {'nagl_model': None,\n",
       "                             'number_of_conformers': None,\n",
       "                             'off_toolkit_backend': 'ambertools',\n",
@@ -218,13 +220,17 @@
       "                         'minimization_steps': 5000,\n",
       "                         'n_replicas': 11,\n",
       "                         'production_length': <Quantity(5.0, 'nanosecond')>,\n",
-      "                         'real_time_analysis_interval': <Quantity(250, 'picosecond')>,\n",
-      "                         'real_time_analysis_minimum_time': <Quantity(500, 'picosecond')>,\n",
+      "                         'real_time_analysis_interval': <Quantity(250.0, 'picosecond')>,\n",
+      "                         'real_time_analysis_minimum_time': <Quantity(500.0, 'picosecond')>,\n",
       "                         'sampler_method': 'repex',\n",
       "                         'sams_flatness_criteria': 'logZ-flatness',\n",
       "                         'sams_gamma0': 1.0,\n",
-      "                         'time_per_iteration': <Quantity(1, 'picosecond')>},\n",
-      " 'solvation_settings': {'solvent_model': 'tip3p',\n",
+      "                         'time_per_iteration': <Quantity(1.0, 'picosecond')>},\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",
@@ -327,6 +333,10 @@
     "    solvation_settings=equil_rfe_settings.OpenMMSolvationSettings(\n",
     "        solvent_model='tip3p',             # Solvent model to generate starting coords\n",
     "        solvent_padding=1.2 * unit.nm,     # Total distance between periodic image starting coords\n",
+    "        box_shape = 'cube',                # Cubic water box\n",
+    "        box_size = None,                   # Size of the water box\n",
+    "        box_vectors = None,                # Box vectors\n",
+    "        number_of_solvent_molecules = None, # Number of solvent molecules\n",
     "    ),\n",
     "    partial_charge_settings=equil_rfe_settings.OpenFFPartialChargeSettings(\n",
     "        partial_charge_method='am1bcc',    # Partial charge method applied - am1bcc\n",
@@ -394,7 +404,9 @@
     "        checkpoint_storage_filename='checkpoint.chk',  # Filename for simulation checkpoints\n",
     "        forcefield_cache='db.json',                 # Cache for small molecule residue templates\n",
     "        output_indices='not water',                 # Do not save water positions\n",
-    "        checkpoint_interval=250 * unit.ps,          # Save a checkpoint every 250 picoseconds\n",
+    "        checkpoint_interval=1 * unit.ns,          # Save a checkpoint every 1 nanoseconds\n",
+    "        positions_write_frequency=100.0 * unit.picosecond, # Save position every 100 picoseconds\n",
+    "        velocities_write_frequency = None, # Don't save velocities\n",
     "    ),\n",
     ")"
    ]
@@ -472,7 +484,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.12.10"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {