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Merged
mikemhenry merged 1 commit into from
Jul 23, 2024
Merged

Issue 138 is no longer relevant #155

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73 changes: 12 additions & 61 deletions cookbook/choose_protocol.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 1,
"id": "38b41f0a-d2a3-4231-bf08-1504d3824978",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -82,7 +82,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 2,
"id": "b0757f5f-e38f-43ac-b43f-ee2bbea95f0d",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -135,7 +135,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 3,
"id": "96c32ead-a8d0-4283-950b-5d27c74ebf16",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -163,7 +163,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 4,
"id": "8d5a6281-50f9-4062-8fa4-375ce2df1bd6",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -252,7 +252,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 5,
"id": "2de6c6a9-bceb-4c9c-ae5a-3d88a72c801a",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -288,7 +288,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 6,
"id": "844e6fa5-f363-47fa-881d-00328faa601c",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -401,7 +401,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 7,
"id": "b499d852-4d7e-47c5-9342-31017baed37c",
"metadata": {
"nbsphinx": "hidden",
Expand All @@ -410,59 +410,10 @@
},
"tags": []
},
"outputs": [
{
"ename": "AssertionError",
"evalue": "",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[15], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m# Double check that the above settings match the defaults - delete this cell if you configure things yourself!\u001b[39;00m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;66;03m# See https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138\u001b[39;00m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m settings \u001b[38;5;241m==\u001b[39m RelativeHybridTopologyProtocol\u001b[38;5;241m.\u001b[39mdefault_settings()\n",
"\u001b[0;31mAssertionError\u001b[0m: "
]
}
],
"source": [
"# Double check that the above settings match the defaults - delete this cell if you configure things yourself!\n",
"# See https://github.com/OpenFreeEnergy/ExampleNotebooks/issues/138\n",
"#assert settings == RelativeHybridTopologyProtocol.default_settings()"
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "3a6d3f17-2049-4456-a315-ce40ebd8969c",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"forcefield_settings\n",
"forcefield_settings=OpenMMSystemGeneratorFFSettings(constraints='hbonds', rigid_water=True, hydrogen_mass=3.0, forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml'], small_molecule_forcefield='openff-2.0.0', nonbonded_cutoff=<Quantity(1.0, 'nanometer')>, nonbonded_method='PME') thermo_settings=ThermoSettings(temperature=<Quantity(298.15, 'kelvin')>, pressure=<Quantity(0.986923267, 'standard_atmosphere')>, ph=None, redox_potential=None) protocol_repeats=3 solvation_settings=OpenMMSolvationSettings(solvent_model='tip3p', solvent_padding=<Quantity(1.2, 'nanometer')>) partial_charge_settings=OpenFFPartialChargeSettings(partial_charge_method='am1bcc', off_toolkit_backend='ambertools', number_of_conformers=None, nagl_model=None) lambda_settings=LambdaSettings(lambda_functions='default', lambda_windows=11) alchemical_settings=AlchemicalSettings(softcore_LJ='gapsys', explicit_charge_correction_cutoff=<Quantity(0.8, 'nanometer')>, endstate_dispersion_correction=False, use_dispersion_correction=False, softcore_alpha=0.85, turn_off_core_unique_exceptions=False, explicit_charge_correction=False) simulation_settings=MultiStateSimulationSettings(equilibration_length=<Quantity(1.0, 'nanosecond')>, production_length=<Quantity(5.0, 'nanosecond')>, minimization_steps=5000, time_per_iteration=<Quantity(1.0, 'picosecond')>, real_time_analysis_interval=<Quantity(250.0, 'picosecond')>, early_termination_target_error=<Quantity(0.0, 'kilocalorie / mole')>, real_time_analysis_minimum_time=<Quantity(500.0, 'picosecond')>, sampler_method='repex', sams_flatness_criteria='logZ-flatness', sams_gamma0=1.0, n_replicas=11) engine_settings=OpenMMEngineSettings(compute_platform=None) integrator_settings=IntegratorSettings(timestep=<Quantity(4.0, 'femtosecond')>, langevin_collision_rate=<Quantity(1.0, '1 / picosecond')>, barostat_frequency=<Quantity(25.0, 'timestep')>, remove_com=False, reassign_velocities=False, n_restart_attempts=20, constraint_tolerance=1e-06) output_settings=MultiStateOutputSettings(checkpoint_interval=<Quantity(250.0, 'picosecond')>, forcefield_cache='db.json', output_indices='not water', checkpoint_storage_filename='checkpoint.chk', output_filename='simulation.nc', output_structure='hybrid_system.pdb'), forcefield_settings != \n",
" forcefield_settings=OpenMMSystemGeneratorFFSettings(constraints='hbonds', rigid_water=True, hydrogen_mass=3.0, forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml', 'amber/phosaa10.xml'], small_molecule_forcefield='openff-2.1.1', nonbonded_cutoff=<Quantity(1.0, 'nanometer')>, nonbonded_method='PME') thermo_settings=ThermoSettings(temperature=<Quantity(298.15, 'kelvin')>, pressure=<Quantity(0.986923267, 'standard_atmosphere')>, ph=None, redox_potential=None) protocol_repeats=3 solvation_settings=OpenMMSolvationSettings(solvent_model='tip3p', solvent_padding=<Quantity(1.2, 'nanometer')>) partial_charge_settings=OpenFFPartialChargeSettings(partial_charge_method='am1bcc', off_toolkit_backend='ambertools', number_of_conformers=None, nagl_model=None) lambda_settings=LambdaSettings(lambda_functions='default', lambda_windows=11) alchemical_settings=AlchemicalSettings(softcore_LJ='gapsys', explicit_charge_correction_cutoff=<Quantity(0.8, 'nanometer')>, endstate_dispersion_correction=False, use_dispersion_correction=False, softcore_alpha=0.85, turn_off_core_unique_exceptions=False, explicit_charge_correction=False) simulation_settings=MultiStateSimulationSettings(equilibration_length=<Quantity(1.0, 'nanosecond')>, production_length=<Quantity(5.0, 'nanosecond')>, minimization_steps=5000, time_per_iteration=<Quantity(1, 'picosecond')>, real_time_analysis_interval=<Quantity(250, 'picosecond')>, early_termination_target_error=<Quantity(0.0, 'kilocalorie_per_mole')>, real_time_analysis_minimum_time=<Quantity(500, 'picosecond')>, sampler_method='repex', sams_flatness_criteria='logZ-flatness', sams_gamma0=1.0, n_replicas=11) engine_settings=OpenMMEngineSettings(compute_platform=None) integrator_settings=IntegratorSettings(timestep=<Quantity(4, 'femtosecond')>, langevin_collision_rate=<Quantity(1.0, '1 / picosecond')>, barostat_frequency=<Quantity(25, 'timestep')>, remove_com=False, reassign_velocities=False, n_restart_attempts=20, constraint_tolerance=1e-06) output_settings=MultiStateOutputSettings(checkpoint_interval=<Quantity(250, 'picosecond')>, forcefield_cache='db.json', output_indices='not water', checkpoint_storage_filename='checkpoint.chk', output_filename='simulation.nc', output_structure='hybrid_system.pdb'), forcefield_settings\n",
"thermo_settings\n",
"protocol_repeats\n",
"solvation_settings\n",
"partial_charge_settings\n",
"lambda_settings\n",
"alchemical_settings\n",
"simulation_settings\n",
"engine_settings\n",
"integrator_settings\n",
"output_settings\n"
]
}
],
"outputs": [],
"source": [
"default_settings = RelativeHybridTopologyProtocol.default_settings()\n",
"\n",
"for name, s in settings:\n",
" print(name)\n",
"\n",
" if getattr(settings, name) != getattr(default_settings, name):\n",
" print(f\"{settings}, {name} != \\n {default_settings}, {name}\")"
"# Double check that the above settings match the defaults\n",
"assert settings == RelativeHybridTopologyProtocol.default_settings()"
]
},
{
Expand All @@ -483,7 +434,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "32b9b58a-d7ea-4071-9046-53e6990a1faa",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -521,7 +472,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.14"
"version": "3.12.4"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down