Add AHFE tutorial

ahfe_tutorial/ahfe_json/benzene.json

@@ -0,0 +1 @@
+{":version:": 1, "__module__": "gufe.transformations.transformation", "__qualname__": "Transformation", "mapping": null, "name": "benzene", "protocol": {":version:": 1, "__module__": "openfe.protocols.openmm_afe.equil_solvation_afe_method", "__qualname__": "AbsoluteSolvationProtocol", "settings": {":is_custom:": true, "__class__": "AbsoluteSolvationSettings", "__module__": "openfe.protocols.openmm_afe.equil_afe_settings", "alchemical_settings": {":is_custom:": true, "__class__": "AlchemicalSettings", "__module__": "openfe.protocols.openmm_afe.equil_afe_settings"}, "integrator_settings": {":is_custom:": true, "__class__": "IntegratorSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "barostat_frequency": {":is_custom:": true, "magnitude": 25, "pint_unit_registry": "openff_units", "unit": "timestep"}, "constraint_tolerance": 1e-06, "langevin_collision_rate": {":is_custom:": true, "magnitude": 1.0, "pint_unit_registry": "openff_units", "unit": "1 / picosecond"}, "n_restart_attempts": 20, "reassign_velocities": false, "remove_com": false, "timestep": {":is_custom:": true, "magnitude": 4, "pint_unit_registry": "openff_units", "unit": "femtosecond"}}, "lambda_settings": {":is_custom:": true, "__class__": "LambdaSettings", "__module__": "openfe.protocols.openmm_afe.equil_afe_settings", "lambda_elec": [0.0, 0.26, 0.5, 0.75, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], "lambda_restraints": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "lambda_vdw": [0.0, 0.0, 0.0, 0.0, 0.0, 0.12, 0.24, 0.36, 0.48, 0.6, 0.7, 0.77, 0.85, 1.0]}, "partial_charge_settings": {":is_custom:": true, "__class__": "OpenFFPartialChargeSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "nagl_model": null, "number_of_conformers": null, "off_toolkit_backend": "ambertools", "partial_charge_method": "am1bcc"}, "protocol_repeats": 1, "solvation_settings": {":is_custom:": true, "__class__": "OpenMMSolvationSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "solvent_model": "tip3p", "solvent_padding": {":is_custom:": true, "magnitude": 1.2, "pint_unit_registry": "openff_units", "unit": "nanometer"}}, "solvent_engine_settings": {":is_custom:": true, "__class__": "OpenMMEngineSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "compute_platform": "CUDA"}, "solvent_equil_output_settings": {":is_custom:": true, "__class__": "MDOutputSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "checkpoint_interval": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "checkpoint_storage_filename": "checkpoint.chk", "equil_npt_structure": "equil_npt_structure.pdb", "equil_nvt_structure": "equil_nvt_structure.pdb", "forcefield_cache": "db.json", "log_output": "equil_simulation.log", "minimized_structure": "minimized.pdb", "output_indices": "not water", "preminimized_structure": "system.pdb", "production_trajectory_filename": "production_equil.xtc", "trajectory_write_interval": {":is_custom:": true, "magnitude": 20, "pint_unit_registry": "openff_units", "unit": "picosecond"}}, "solvent_equil_simulation_settings": {":is_custom:": true, "__class__": "MDSimulationSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "equilibration_length": {":is_custom:": true, "magnitude": 0.2, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "equilibration_length_nvt": {":is_custom:": true, "magnitude": 0.1, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "minimization_steps": 5000, "production_length": {":is_custom:": true, "magnitude": 0.5, "pint_unit_registry": "openff_units", "unit": "nanosecond"}}, "solvent_forcefield_settings": {":is_custom:": true, "__class__": "OpenMMSystemGeneratorFFSettings", "__module__": "gufe.settings.models", "constraints": "hbonds", "forcefields": ["amber/ff14SB.xml", "amber/tip3p_standard.xml", "amber/tip3p_HFE_multivalent.xml", "amber/phosaa10.xml"], "hydrogen_mass": 3.0, "nonbonded_cutoff": {":is_custom:": true, "magnitude": 1.0, "pint_unit_registry": "openff_units", "unit": "nanometer"}, "nonbonded_method": "PME", "rigid_water": true, "small_molecule_forcefield": "openff-2.0.0"}, "solvent_output_settings": {":is_custom:": true, "__class__": "MultiStateOutputSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "checkpoint_interval": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "checkpoint_storage_filename": "solvent_checkpoint.nc", "forcefield_cache": "db.json", "output_filename": "solvent.nc", "output_indices": "not water", "output_structure": "hybrid_system.pdb"}, "solvent_simulation_settings": {":is_custom:": true, "__class__": "MultiStateSimulationSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "early_termination_target_error": {":is_custom:": true, "magnitude": 0.0, "pint_unit_registry": "openff_units", "unit": "kilocalorie_per_mole"}, "equilibration_length": {":is_custom:": true, "magnitude": 0.009999999999999998, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "minimization_steps": 5000, "n_replicas": 14, "production_length": {":is_custom:": true, "magnitude": 0.4999999999999999, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "real_time_analysis_interval": {":is_custom:": true, "magnitude": 250, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "real_time_analysis_minimum_time": {":is_custom:": true, "magnitude": 500, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "sampler_method": "repex", "sams_flatness_criteria": "logZ-flatness", "sams_gamma0": 1.0, "time_per_iteration": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}}, "thermo_settings": {":is_custom:": true, "__class__": "ThermoSettings", "__module__": "gufe.settings.models", "ph": null, "pressure": {":is_custom:": true, "magnitude": 0.9869232667160129, "pint_unit_registry": "openff_units", "unit": "standard_atmosphere"}, "redox_potential": null, "temperature": {":is_custom:": true, "magnitude": 298.15, "pint_unit_registry": "openff_units", "unit": "kelvin"}}, "vacuum_engine_settings": {":is_custom:": true, "__class__": "OpenMMEngineSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "compute_platform": null}, "vacuum_equil_output_settings": {":is_custom:": true, "__class__": "MDOutputSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "checkpoint_interval": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "checkpoint_storage_filename": "checkpoint.chk", "equil_npt_structure": "equil_structure.pdb", "equil_nvt_structure": null, "forcefield_cache": "db.json", "log_output": "equil_simulation.log", "minimized_structure": "minimized.pdb", "output_indices": "not water", "preminimized_structure": "system.pdb", "production_trajectory_filename": "production_equil.xtc", "trajectory_write_interval": {":is_custom:": true, "magnitude": 20, "pint_unit_registry": "openff_units", "unit": "picosecond"}}, "vacuum_equil_simulation_settings": {":is_custom:": true, "__class__": "MDSimulationSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "equilibration_length": {":is_custom:": true, "magnitude": 0.2, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "equilibration_length_nvt": null, "minimization_steps": 5000, "production_length": {":is_custom:": true, "magnitude": 0.5, "pint_unit_registry": "openff_units", "unit": "nanosecond"}}, "vacuum_forcefield_settings": {":is_custom:": true, "__class__": "OpenMMSystemGeneratorFFSettings", "__module__": "gufe.settings.models", "constraints": "hbonds", "forcefields": ["amber/ff14SB.xml", "amber/tip3p_standard.xml", "amber/tip3p_HFE_multivalent.xml", "amber/phosaa10.xml"], "hydrogen_mass": 3.0, "nonbonded_cutoff": {":is_custom:": true, "magnitude": 1.0, "pint_unit_registry": "openff_units", "unit": "nanometer"}, "nonbonded_method": "nocutoff", "rigid_water": true, "small_molecule_forcefield": "openff-2.0.0"}, "vacuum_output_settings": {":is_custom:": true, "__class__": "MultiStateOutputSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "checkpoint_interval": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "checkpoint_storage_filename": "vacuum_checkpoint.nc", "forcefield_cache": "db.json", "output_filename": "vacuum.nc", "output_indices": "not water", "output_structure": "hybrid_system.pdb"}, "vacuum_simulation_settings": {":is_custom:": true, "__class__": "MultiStateSimulationSettings", "__module__": "openfe.protocols.openmm_utils.omm_settings", "early_termination_target_error": {":is_custom:": true, "magnitude": 0.0, "pint_unit_registry": "openff_units", "unit": "kilocalorie_per_mole"}, "equilibration_length": {":is_custom:": true, "magnitude": 0.009999999999999998, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "minimization_steps": 5000, "n_replicas": 14, "production_length": {":is_custom:": true, "magnitude": 0.4999999999999999, "pint_unit_registry": "openff_units", "unit": "nanosecond"}, "real_time_analysis_interval": {":is_custom:": true, "magnitude": 250, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "real_time_analysis_minimum_time": {":is_custom:": true, "magnitude": 500, "pint_unit_registry": "openff_units", "unit": "picosecond"}, "sampler_method": "repex", "sams_flatness_criteria": "logZ-flatness", "sams_gamma0": 1.0, "time_per_iteration": {":is_custom:": true, "magnitude": 1, "pint_unit_registry": "openff_units", "unit": "picosecond"}}}}, "stateA": {":version:": 1, "__module__": "gufe.chemicalsystem", "__qualname__": "ChemicalSystem", "components": {"ligand": {":version:": 1, "__module__": "gufe.components.smallmoleculecomponent", "__qualname__": "SmallMoleculeComponent", "atoms": [[6, 0, 0, true, 0, 0, {}], [6, 0, 0, true, 0, 0, {}], [6, 0, 0, true, 0, 0, {}], [6, 0, 0, true, 0, 0, {}], [6, 0, 0, true, 0, 0, {}], [6, 0, 0, true, 0, 0, {}], [1, 0, 0, false, 0, 0, {}], [1, 0, 0, false, 0, 0, {}], [1, 0, 0, false, 0, 0, {}], [1, 0, 0, false, 0, 0, {}], [1, 0, 0, false, 0, 0, {}], [1, 0, 0, false, 0, 0, {}]], "bonds": [[0, 1, 12, 0, {}], [0, 5, 12, 0, {}], [0, 6, 1, 0, {}], [1, 2, 12, 0, {}], [1, 7, 1, 0, {}], [2, 3, 12, 0, {}], [2, 8, 1, 0, {}], [3, 4, 12, 0, {}], [3, 9, 1, 0, {}], [4, 5, 12, 0, {}], [4, 10, 1, 0, {}], [5, 11, 1, 0, {}]], "conformer": ["\u0093NUMPY\u0001\u0000v\u0000{'descr': '<f8', 'fortran_order': False, 'shape': (12, 3), }                                                         \n\u00ee|?5^\u00fa9@\u0002+\u0087\u0016\u00d9N\u0015@\u0004V\u000e-\u00b2\u001d\u0013@\u0085\u00ebQ\u00b8\u001ee:@\u00b2\u009d\u00ef\u00a7\u00c6K\u0014@\u00cb\u00a1E\u00b6\u00f3\u00fd\u000b@\u00d7\u00a3p=\nW;@q=\n\u00d7\u00a3p\u0017@\u009e\u00ef\u00a7\u00c6K7\u0007@\u0083\u00c0\u00ca\u00a1E\u00d6;@\u00c9v\u00be\u009f\u001a\u00af\u001b@Zd;\u00dfO\u008d\f@\u00ecQ\u00b8\u001e\u0085k;@b\u0010X9\u00b4\u00c8\u001c@\u0006\u0081\u0095C\u008bl\u0013@sh\u0091\u00ed|\u007f:@j\u00bct\u0093\u0018\u0084\u0019@\u00c7K7\u0089A\u00e0\u0015@\u00ed\u009e<,\u00d4:9@<N\u00d1\u0091\\\u00be\u0012@\u0097\u00ff\u0090~\u00fb\u00fa\u0014@\u000f\u009c3\u00a2\u00b4\u00f79@\u008d(\u00ed\r\u00be\u00f0\u0010@\u00f0\u0016HP\u00fc\u0098\u0007@\u00aa\u00f1\u00d2Mb\u00b0;@\u00bc\u0005\u0012\u0014?\u0086\u0016@\u00c3d\u00aa`TR\u00fe?\u00a6\u009b\u00c4 \u00b0\u0092<@\u00dd$\u0006\u0081\u0095C\u001e@K\u00ea\u00044\u0011\u00b6\b@RI\u009d\u0080&\u00d2;@\u0002\u009a\b\u001b\u009e\u001e @z\u00c7):\u0092\u008b\u0015@9EGr\u00f9/:@}?5^\u00baI\u001a@]m\u00c5\u00fe\u00b2\u00fb\u0019@", {}], "molprops": {"ofe-name": "benzene"}}, "solvent": {":version:": 1, "__module__": "gufe.components.solventcomponent", "__qualname__": "SolventComponent", "ion_concentration": "0.15 molar", "negative_ion": "Cl-", "neutralize": true, "positive_ion": "Na+", "smiles": "O"}}, "name": "benzene"}, "stateB": {":version:": 1, "__module__": "gufe.chemicalsystem", "__qualname__": "ChemicalSystem", "components": {"solvent": {":version:": 1, "__module__": "gufe.components.solventcomponent", "__qualname__": "SolventComponent", "ion_concentration": "0.15 molar", "negative_ion": "Cl-", "neutralize": true, "positive_ion": "Na+", "smiles": "O"}}, "name": ""}}