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IAlibayIAlibay
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Update md inputs for v1.7
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Lines changed: 89 additions & 30 deletions

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‎openmm_md/plain_md.ipynb‎

Lines changed: 89 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -137,7 +137,16 @@
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"execution_count": 1,
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"id": "20fc8142-c618-4d50-b903-5a04f6a34d5c",
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/openmoltools/utils.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
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" from pkg_resources import resource_filename\n"
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]
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}
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],
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"source": [
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"import openfe\n",
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"from openfe import ChemicalSystem, ProteinComponent, SmallMoleculeComponent, SolventComponent\n",
@@ -186,7 +195,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 3,
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"id": "b27e54cc-fd6a-4afc-ab22-4dde0561938c",
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"metadata": {},
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"outputs": [],
@@ -200,12 +209,13 @@
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"# Setting the production length and checkpoint interval to 20 ps to match the trajectory write interval, so one frame will be written\n",
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"settings.simulation_settings.production_length = 0.02 * unit.nanosecond # setting the npt production length to 20 ps\n",
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"settings.output_settings.checkpoint_interval = 0.02 * unit.nanosecond # setting the checkpoint interval to 20 ps\n",
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"settings.engine_settings.compute_platform = 'CPU' # running the simulation on the cpu"
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"settings.engine_settings.compute_platform = 'CPU' # running the simulation on the cpu\n",
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"settings.solvation_settings.solvent_padding = 1.0 * unit.nanometer # set the solvent padding to 1 nm to reduce the number of waters"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 4,
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"id": "b69668c9-2e74-421e-a9ea-b7f3bc6c6e5a",
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"metadata": {},
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"outputs": [
@@ -220,18 +230,20 @@
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" 'amber/tip3p_HFE_multivalent.xml',\n",
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" 'amber/phosaa10.xml'],\n",
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" 'hydrogen_mass': 3.0,\n",
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" 'nonbonded_cutoff': <Quantity(1.0, 'nanometer')>,\n",
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" 'nonbonded_cutoff': {'unit': 'nanometer', 'val': 0.9},\n",
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" 'nonbonded_method': 'PME',\n",
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" 'rigid_water': True,\n",
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" 'small_molecule_forcefield': 'openff-2.1.1'},\n",
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" 'integrator_settings': {'barostat_frequency': <Quantity(25.0, 'timestep')>,\n",
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" 'small_molecule_forcefield': 'openff-2.2.1'},\n",
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" 'integrator_settings': {'barostat_frequency': {'unit': 'timestep',\n",
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" 'val': 25.0},\n",
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" 'constraint_tolerance': 1e-06,\n",
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" 'langevin_collision_rate': <Quantity(1.0, '1 / picosecond')>,\n",
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" 'langevin_collision_rate': {'unit': '1 / picosecond',\n",
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" 'val': 1.0},\n",
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" 'n_restart_attempts': 20,\n",
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" 'reassign_velocities': False,\n",
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" 'remove_com': False,\n",
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" 'timestep': <Quantity(4.0, 'femtosecond')>},\n",
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" 'output_settings': {'checkpoint_interval': <Quantity(20.0, 'picosecond')>,\n",
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" 'timestep': {'unit': 'femtosecond', 'val': 4.0}},\n",
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" 'output_settings': {'checkpoint_interval': {'unit': 'nanosecond', 'val': 0.02},\n",
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" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
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" 'equil_npt_structure': 'equil_npt.pdb',\n",
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" 'equil_nvt_structure': 'equil_nvt.pdb',\n",
@@ -241,26 +253,38 @@
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" 'output_indices': 'not water',\n",
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" 'preminimized_structure': 'system.pdb',\n",
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" 'production_trajectory_filename': 'simulation.xtc',\n",
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" 'trajectory_write_interval': <Quantity(20.0, 'picosecond')>},\n",
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" 'trajectory_write_interval': {'unit': 'picosecond',\n",
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" 'val': 20.0}},\n",
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" 'partial_charge_settings': {'nagl_model': None,\n",
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" 'number_of_conformers': None,\n",
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" 'off_toolkit_backend': 'ambertools',\n",
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" 'partial_charge_method': 'am1bcc'},\n",
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" 'protocol_repeats': 1,\n",
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" 'simulation_settings': {'equilibration_length': <Quantity(0.01, 'nanosecond')>,\n",
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" 'equilibration_length_nvt': <Quantity(0.01, 'nanosecond')>,\n",
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" 'simulation_settings': {'equilibration_length': {'unit': 'nanosecond',\n",
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" 'val': 0.01},\n",
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" 'equilibration_length_nvt': {'unit': 'nanosecond',\n",
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" 'val': 0.01},\n",
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" 'minimization_steps': 5000,\n",
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" 'production_length': <Quantity(0.02, 'nanosecond')>},\n",
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" 'solvation_settings': {'box_shape': 'cube',\n",
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" 'production_length': {'unit': 'nanosecond',\n",
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" 'val': 0.02}},\n",
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" 'solvation_settings': {'box_shape': 'dodecahedron',\n",
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" 'box_size': None,\n",
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" 'box_vectors': None,\n",
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" 'number_of_solvent_molecules': None,\n",
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" 'solvent_model': 'tip3p',\n",
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" 'solvent_padding': <Quantity(1.2, 'nanometer')>},\n",
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" 'solvent_padding': {'unit': 'nanometer', 'val': 1.0}},\n",
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" 'thermo_settings': {'ph': None,\n",
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" 'pressure': <Quantity(0.986923267, 'standard_atmosphere')>,\n",
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" 'pressure': {'unit': 'bar', 'val': 1},\n",
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" 'redox_potential': None,\n",
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" 'temperature': <Quantity(298.15, 'kelvin')>}}\n"
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" 'temperature': {'unit': 'kelvin', 'val': 298.15}}}\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/gufe/settings/models.py:30: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/\n",
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" pprint.pprint(self.dict())\n"
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]
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}
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],
@@ -282,7 +306,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 5,
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"id": "3b0f5a26-b23b-4ab2-9f1e-293d98ed5bcd",
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"metadata": {},
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"outputs": [],
@@ -303,7 +327,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 6,
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"id": "987cceda-1253-417b-8cca-bc750ac0aa1e",
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"metadata": {},
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"outputs": [],
@@ -342,7 +366,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 7,
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"id": "7689c7ba-39a2-49ea-b82b-e3b198354c5b",
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"metadata": {},
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"outputs": [],
@@ -353,7 +377,7 @@
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"md_dir.mkdir(exist_ok=True)\n",
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"\n",
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"# then we write out the transformation\n",
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"nontransformation.dump(md_dir / f\"{nontransformation.name}.json\")"
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"nontransformation.to_json(md_dir / f\"{nontransformation.name}.json\")"
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]
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},
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{
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": 8,
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"id": "544d037d-3a53-4390-91b8-3104c00694f0",
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"metadata": {
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"editable": true,
@@ -395,9 +419,36 @@
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/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",
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"INFO:openfe.utils.system_probe.log:SYSTEM CONFIG DETAILS:\n",
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"INFO:openfe.utils.system_probe.log.hostname:hostname: 'sith'\n",
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"INFO:openfe.utils.system_probe.log.gpu:CUDA-based GPU not found\n",
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"INFO:openfe.utils.system_probe.log:Memory used: 7.3G (25.9%)\n",
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"INFO:openfe.utils.system_probe.log:scratch_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0: 82% full (53.4G free)\n",
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"INFO:gufekey.openfe.protocols.openmm_md.plain_md_methods.PlainMDProtocolUnit:Creating system\n",
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"INFO:openmmforcefields.generators.template_generators:Requested to generate parameters for residue <Residue 0 (UNK) of chain 0>\n",
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"INFO:openmmforcefields.generators.template_generators:Generating a residue template for [H][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H] using openff-2.2.1\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 0\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 1\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 2\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 3\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 4\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 5\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 6\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 7\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 8\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 9\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 10\n",
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"INFO:openff.interchange.smirnoff._nonbonded:Preset charges applied to atom index 11\n",
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"/home/ialibay/github/openfe/openfe/protocols/openmm_utils/omm_compute.py:76: UserWarning: Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n",
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" warnings.warn(wmsg)\n",
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"WARNING:root:Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n"
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"WARNING:root:Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:minimizing systems\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:Running NVT equilibration\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:Completed NVT equilibration in 93.03289294242859 seconds\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:Running NPT equilibration\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:Completed NPT equilibration in 105.741370677948 seconds\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:running production phase\n",
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"INFO:openfe.protocols.openmm_md.plain_md_methods:Completed simulation in 216.3571000099182 seconds\n"
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]
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}
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],
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 10,
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"id": "16fbf816-8d3d-4121-ab0e-5cd7741788d6",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"text": [
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"checkpoint.chk equil_npt.pdb minimized.pdb simulation.xtc\n",
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"db.json equil_nvt.pdb simulation.log system.pdb\n"
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"checkpoint.chk\tequil_npt.pdb minimized.pdb simulation.xtc\n",
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"db.json\t\tequil_nvt.pdb simulation.log system.pdb\n"
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]
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},
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{
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"name": "stderr",
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"text": [
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"/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/pty.py:95: DeprecationWarning: This process (pid=257465) is multi-threaded, use of forkpty() may lead to deadlocks in the child.\n",
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" pid, fd = os.forkpty()\n"
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]
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}
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],
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"source": [
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"!ls shared_PlainMDProtocolUnit-256e9093d8f3443b9949b95e7ddbb64e_attempt_0/"
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"!ls shared_PlainMDProtocolUnit-6b85013e6cb94120baf447540650643b_attempt_0/"
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]
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},
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{
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.8"
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"version": "3.12.11"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

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