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Update some settings in the MD tutorial to get outputs #201

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Merged
IAlibay merged 3 commits into from
Apr 28, 2025
Merged

Update some settings in the MD tutorial to get outputs #201

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fefa8d5
Update some settings to get outputs
hannahbaumann Apr 23, 2025
a53aa7c
Merge branch 'main' into update-md-tutorial
IAlibay Apr 23, 2025
3297cd1
Update openmm_md/plain_md.ipynb
hannahbaumann Apr 28, 2025
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45 changes: 30 additions & 15 deletions openmm_md/plain_md.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,7 @@
"id": "7266db2c-37e5-419a-9015-929ea1635d98",
"metadata": {},
"source": [
"In this notebook we run an MD simulation of benzene bound to T4-lysozyme L99A.",
"![image](assets/t4lyso.png)"
"In this notebook we run an MD simulation of benzene bound to T4-lysozyme L99A.![image](assets/t4lyso.png)"
]
},
{
Expand Down Expand Up @@ -147,7 +146,9 @@
"settings = PlainMDProtocol.default_settings()\n",
"settings.simulation_settings.equilibration_length_nvt = 0.01 * unit.nanosecond # setting the nvt equilibration length to 10 ps\n",
"settings.simulation_settings.equilibration_length = 0.01 * unit.nanosecond # setting the npt equilibration length to 10 ps\n",
"settings.simulation_settings.production_length = 0.01 * unit.nanosecond # setting the npt production length to 10 ps\n",
"# Setting the production length and checkpoint interval to 20 ps to match the trajectory write interval, so one frame will be written\n",
"settings.simulation_settings.production_length = 0.02 * unit.nanosecond # setting the npt production length to 20 ps\n",
"settings.output_settings.checkpoint_interval = 0.02 * unit.nanosecond # setting the checkpoint interval to 20 ps\n",
"settings.engine_settings.compute_platform = 'CPU' # running the simulation on the cpu"
]
},
Expand All @@ -161,7 +162,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
"{'engine_settings': {'compute_platform': 'CPU'},\n",
"{'engine_settings': {'compute_platform': 'CPU', 'gpu_device_index': None},\n",
" 'forcefield_settings': {'constraints': 'hbonds',\n",
" 'forcefields': ['amber/ff14SB.xml',\n",
" 'amber/tip3p_standard.xml',\n",
Expand All @@ -171,15 +172,15 @@
" 'nonbonded_cutoff': <Quantity(1.0, 'nanometer')>,\n",
" 'nonbonded_method': 'PME',\n",
" 'rigid_water': True,\n",
" 'small_molecule_forcefield': 'openff-2.0.0'},\n",
" 'integrator_settings': {'barostat_frequency': <Quantity(25, 'timestep')>,\n",
" 'small_molecule_forcefield': 'openff-2.1.1'},\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",
" 'output_settings': {'checkpoint_interval': <Quantity(1, 'picosecond')>,\n",
" 'timestep': <Quantity(4.0, 'femtosecond')>},\n",
" 'output_settings': {'checkpoint_interval': <Quantity(20.0, 'picosecond')>,\n",
" 'checkpoint_storage_filename': 'checkpoint.chk',\n",
" 'equil_npt_structure': 'equil_npt.pdb',\n",
" 'equil_nvt_structure': 'equil_nvt.pdb',\n",
Expand All @@ -189,7 +190,7 @@
" 'output_indices': 'not water',\n",
" 'preminimized_structure': 'system.pdb',\n",
" 'production_trajectory_filename': 'simulation.xtc',\n",
" 'trajectory_write_interval': <Quantity(20, 'picosecond')>},\n",
" 'trajectory_write_interval': <Quantity(20.0, 'picosecond')>},\n",
" 'partial_charge_settings': {'nagl_model': None,\n",
" 'number_of_conformers': None,\n",
" 'off_toolkit_backend': 'ambertools',\n",
Expand All @@ -198,8 +199,12 @@
" 'simulation_settings': {'equilibration_length': <Quantity(0.01, 'nanosecond')>,\n",
" 'equilibration_length_nvt': <Quantity(0.01, 'nanosecond')>,\n",
" 'minimization_steps': 5000,\n",
" 'production_length': <Quantity(0.01, 'nanosecond')>},\n",
" 'solvation_settings': {'solvent_model': 'tip3p',\n",
" 'production_length': <Quantity(0.02, 'nanosecond')>},\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 @@ -286,7 +291,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 6,
"id": "7689c7ba-39a2-49ea-b82b-e3b198354c5b",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -325,7 +330,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "544d037d-3a53-4390-91b8-3104c00694f0",
"metadata": {
"editable": true,
Expand All @@ -334,7 +339,17 @@
},
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/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",
" warnings.warn(wmsg)\n",
"WARNING:root:Non-CUDA platform selected: CPU, this may significantly impact simulation performance\n"
]
}
],
"source": [
"import gufe\n",
"import pathlib\n",
Expand Down Expand Up @@ -407,7 +422,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.13"
"version": "3.12.8"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
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