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@mattwthompson
mattwthompson committed Nov 9, 2023
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50 changes: 26 additions & 24 deletions examples/virtual_sites/vsite_showcase.ipynb
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{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "f531ab0129bd48dd9ac2c99b6f99905c",
"model_id": "ba621889dffa475e80a6a6b5f8f476e5",
"version_major": 2,
"version_minor": 0
},
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"output_type": "stream",
"text": [
"Starting simulation\n",
"Elapsed time 0.89 seconds\n",
"Elapsed time 0.96 seconds\n",
"Done!\n"
]
}
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{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "5b1b2dbed8b04107b9d8ded035dce21b",
"model_id": "c05515b6f75647ed89ebf066d9f99c48",
"version_major": 2,
"version_minor": 0
},
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"source": [
"Parameterizes a water box with OpenFF/SMIRNOFF and OpenMM implementations of TIP5P.\n",
"\n",
"The code examines the geometry and energy between the two, and examines cases where minimization is performed.\n",
"Specifically, the code compares the four possible combinations:\n",
" - SMIRONFF and OpenMM geometry/energy, minimized separately and then compared\n",
" - SMIRNOFF and OpenMM geometry/energy using no minimization\n",
" - Geometry minimized using OpenFF, then a single point energy calculation is done with OpenMM\n",
" - Geometry minimized using OpenFF, then a single point energy calculation is done with OpenFF\n",
"This code examines the geometry and energy between the two, and examines cases where minimization is performed.\n",
"\n",
"The virtual site definitions give rise to small differences in geometry in due to to how they are defined from their parent atoms.\n",
"OpenMM's force field results in `openmm.OutOfPlaneSite`s being createdwhereas OpenFF's force field results in `openmm.LocalCoordinatesSite`s.\n",
"The virtual site definitions give rise to small differences in geometry in due to to how they are defined relative to their parent atoms.\n",
"OpenMM's force field produces `openmm.OutOfPlaneSite`s whereas OpenFF's force field produces in `openmm.LocalCoordinatesSite`s.\n",
"(In each case, these objects are OpenMM objects to be used in OpenMM simulations; implementations in other engines are not covered here.)\n",
"`OutOfPlaneSite` virtual sites' positions are are determined based on the positions of the orientation atoms.\n",
"(In water models, the \"parent\" atom is oxygen and the \"orientation\" atoms are the oxygen and hydrogens; in other chemistries virtual sites may be definited differently.)\n",
"`LocalCoordinatesSite` virtual sites' positions relative to orientation atoms are fixed to a constant value in order to adhere to the SMIRNOFF specification.\n",
"A consequence of this difference is that tiny fluctuations in the molecular geometry cause slightly different energy evaluations.\n",
"This can arise from marginally different initial positions or dynamics over the course of a simulation, but the description at equilibrium should match.\n",
"A consequence of this difference is that tiny fluctuations in the molecular geometry cause slightly different coordinates and, therefore, energy evaluations.\n",
"This can arise from marginally different initial positions or from the dynamics of a simulation, but the descriptions at equilibrium should match.\n",
"Further nuance is described in the [OpenMM User Guide](http://docs.openmm.org/8.0.0/userguide/theory/05_other_features.html#virtual-sites) and API docs.\n",
"\n",
"This example uses water molecules, but both OpenFF and OpenMM infrastructure support a variety of other virtual site definitions for use in other chemistries.\n",
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"\n",
" print(\n",
" f\"Results for: {name}\\n\"\n",
" f\"Energy difference ({_energy_difference.units}):\\n\\t{_energy_difference.m}\\n\"\n",
" f\"Coordinates difference ({coordinate_difference.units}), norm):\\n\\t{coordinate_difference.m}\\n\"\n",
" f\"Energy difference ({_energy_difference.units}):\\n\\t\"\n",
" f\"{_energy_difference.m:0.3e}\\n\"\n",
" f\"Coordinates difference ({coordinate_difference.units}), norm):\\n\\t\"\n",
" f\"{coordinate_difference.m:0.3e}\\n\"\n",
" )"
]
},
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},
"outputs": [],
"source": [
"# The TIP5P force field in SMIRNOFF format\n",
"# The TIP5P force field in SMIRNOFF format, provided by the OpenFF Toolkit\n",
"openff_force_field = ForceField(\"tip5p.offxml\")\n",
"\n",
"# The OpenMM definition of tip5p\n",
"# The OpenMM definition of TIP5P\n",
"openmm_force_field = openmm.app.ForceField(\"tip5p.xml\")"
]
},
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"text": [
"Results for: OpenFF - OpenMM comparison (per molecule)\n",
"Energy difference (kilojoule / mole):\n",
"\t1.9073486328125e-06\n",
"\t1.907e-06\n",
"Coordinates difference (angstrom), norm):\n",
"\t1.6239076780209112e-07\n",
"\t1.624e-07\n",
"\n"
]
}
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"num_duplicates = (2, 1, 1) # 2x2x2 = 8 water molecules\n",
"spacing = (3.0, 3.0, 3.0) # water spaced 3A apart in each direction\n",
"\n",
"numpy.set_printoptions(formatter={\"float_kind\": \"{:13.10f}\".format})\n",
"\n",
"waters = build_water_lattice(num_duplicates, spacing)\n",
"\n",
"off_crds, off_ene = evaluate_openff(waters, openff_force_field, minimize=minimize)\n",
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"omm_crds = numpy.array(omm_crds.value_in_unit(openmm.unit.angstrom))\n",
"\n",
"coordinate_difference = Quantity(\n",
" numpy.linalg.norm(off_crds - omm_crds[reorder(numpy.prod(num_duplicates)), :])\n",
" / numpy.prod(num_duplicates),\n",
" numpy.linalg.norm(off_crds - omm_crds[reorder(numpy.prod(num_duplicates)), :]),\n",
" unit.angstrom,\n",
")\n",
"coordinate_difference /= numpy.prod(num_duplicates)\n",
"energy_difference = abs(off_ene - omm_ene) / numpy.prod(num_duplicates)\n",
"\n",
"print_info(\n",
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" energy_difference < 1e-4 * openmm.unit.kilojoule_per_mole\n",
"), f\"Energies differ by {energy_difference}\""
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.9.18"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
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