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Merged
IAlibay merged 3 commits into from
Jul 31, 2025
Merged

Adapt host min/max distance restraints + fix broken notebook #221

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3f65928
SepTop: Adapt host min/max distance
hannahbaumann Jul 31, 2025
fddb5c5
Fix broken test
hannahbaumann Jul 31, 2025
43049c6
Also adapt settings ABFE protocol
hannahbaumann Jul 31, 2025
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34 changes: 23 additions & 11 deletions cookbook/choose_protocol.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
")"
]
Expand Down Expand Up @@ -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": {
Expand Down
33 changes: 14 additions & 19 deletions openmm_septop/septop_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"Generating charges: 100%|███████████████████████| 10/10 [02:53<00:00, 17.38s/it]\n"
"Generating charges: 100%|███████████████████████| 10/10 [02:54<00:00, 17.43s/it]\n"
]
}
],
Expand Down Expand Up @@ -378,7 +378,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 12,
"id": "c2b3de6d-1f11-432d-82f3-9deff16c78dc",
"metadata": {},
"outputs": [],
Expand All @@ -388,14 +388,17 @@
"\n",
"# Run only a single repeat\n",
"settings.protocol_repeats = 1\n",
"# Change the min and max distance between protein and ligand atoms for Boresch restraints to avoid periodicity issues\n",
"settings.complex_restraint_settings.host_min_distance = 0.5 * unit.nanometer\n",
"settings.complex_restraint_settings.host_max_distance = 1.5 * unit.nanometer\n",
"# Set the equilibration time to 2 ns (which is also the default)\n",
"settings.solvent_simulation_settings.equilibration_length = 2000 * unit.picosecond\n",
"settings.complex_simulation_settings.equilibration_length = 2000 * unit.picosecond"
]
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 13,
"id": "7adf42d6",
"metadata": {},
"outputs": [],
Expand All @@ -415,7 +418,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 14,
"id": "44ba94ca",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -452,7 +455,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 15,
"id": "66666a80",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -497,7 +500,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 16,
"id": "d6cebd9a",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -539,7 +542,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 17,
"id": "b96b57a9",
"metadata": {},
"outputs": [
Expand All @@ -558,7 +561,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/pty.py:95: DeprecationWarning: This process (pid=12534) is multi-threaded, use of forkpty() may lead to deadlocks in the child.\n",
"/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/pty.py:95: DeprecationWarning: This process (pid=26930) is multi-threaded, use of forkpty() may lead to deadlocks in the child.\n",
" pid, fd = os.forkpty()\n"
]
}
Expand Down Expand Up @@ -606,7 +609,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 18,
"id": "de7d7920-b171-42fe-9b82-5ff5694d26e5",
"metadata": {},
"outputs": [],
Expand All @@ -624,7 +627,7 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 19,
"id": "0e2e0727-2c4a-4b60-947c-44504aed2eee",
"metadata": {},
"outputs": [
Expand All @@ -637,22 +640,14 @@
" 'pint_unit_registry': 'openff_units'}"
]
},
"execution_count": 20,
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"estimate"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b70822d2-5030-4ed9-87da-f166de551592",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down
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