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Not only querying, but also modifying system parameters #18
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6a01959
Modifying parameter
yuanqing-wang e7b035c
title change
yuanqing-wang 4266d19
start implementing own functional forms
yuanqing-wang 5681941
get energy components
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trash clean
yuanqing-wang c938c42
Merge branch 'main' of https://github.com/yuanqing-wang/openmm-cookbook
yuanqing-wang 7c6d594
Update Use OpenMM to Verify Your MM Functional Form Implementation.ipynb
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trash cleaning
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merged modifying parameters into querying parameters
yuanqing-wang 9c47ba7
moved benchmarking script into another PR; fixed typo; added querying…
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Merge branch 'openmm:main' into main
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minor fixes; update parameters in `Context`
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notebooks/cookbook/Modifying Parameters in an OpenMM System.ipynb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,322 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "5cc09957", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Modifying Parameters in System\n", | ||
| "\n", | ||
| "Some machine learning force field construction schemes, such as [Espaloma](https://pubs.rsc.org/en/content/articlehtml/2022/sc/d2sc02739a), would output parameters which can be picked up by the parameter-holding `System` object of OpenMM, which could be further used in molecular dynamics (MD) simulations just like a vanilla `System`.\n", | ||
| "In this tutorial, we show how you can modify the parameters of `System` object so you can write your own machine learning force field API.\n", | ||
| "\n", | ||
| "This example is inspired by the [Espaloma deployment](https://github.com/choderalab/espaloma/blob/master/espaloma/graphs/deploy.py) implementation." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "5003093c", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "First, let's load a PDB file and use Amber14 force field as placeholder parameters." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "9c163ab2", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from openmm.app import *\n", | ||
| "from openmm import *\n", | ||
| "\n", | ||
| "pdb = PDBFile('ala_ala_ala.pdb')\n", | ||
| "forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')\n", | ||
| "system = forcefield.createSystem(pdb.topology)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "0c5c2c35", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now we loop through the forces to get bonded components of the energy." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "f92baca2", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "forces = list(system.getForces())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "id": "e8b4bef3", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "harmonic_bond_force = [force for force in forces if \"HarmonicBondForce\" in force.__class__.__name__].pop()\n", | ||
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|
||
| "harmonic_angle_force = [force for force in forces if \"HarmonicAngleForce\" in force.__class__.__name__].pop()\n", | ||
| "periodic_torsion_force = [force for force in forces if \"PeriodicTorsionForce\" in force.__class__.__name__].pop()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "0d8cde7e", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "We can inspect each component to get a list of indices and parameters." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "425b070e", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "- Bonds:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 9, | ||
| "id": "b09324e6", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Bond between 10 and 4 has equilibrium length 0.1522 nm and force constant 265265.6 kJ/(nm**2 mol).\n", | ||
| "Bond between 10 and 11 has equilibrium length 0.12290000000000001 nm and force constant 476975.9999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 4 and 6 has equilibrium length 0.1526 nm and force constant 259407.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 4 and 5 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 4 and 0 has equilibrium length 0.1471 nm and force constant 307105.5999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 6 and 7 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 6 and 8 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 6 and 9 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 1 and 0 has equilibrium length 0.101 nm and force constant 363171.19999999995 kJ/(nm**2 mol).\n", | ||
| "Bond between 2 and 0 has equilibrium length 0.101 nm and force constant 363171.19999999995 kJ/(nm**2 mol).\n", | ||
| "Bond between 3 and 0 has equilibrium length 0.101 nm and force constant 363171.19999999995 kJ/(nm**2 mol).\n", | ||
| "Bond between 10 and 12 has equilibrium length 0.1335 nm and force constant 410031.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 20 and 14 has equilibrium length 0.1522 nm and force constant 265265.6 kJ/(nm**2 mol).\n", | ||
| "Bond between 20 and 21 has equilibrium length 0.12290000000000001 nm and force constant 476975.9999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 14 and 16 has equilibrium length 0.1526 nm and force constant 259407.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 14 and 15 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 14 and 12 has equilibrium length 0.1449 nm and force constant 282001.5999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 16 and 17 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 16 and 18 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 16 and 19 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 13 and 12 has equilibrium length 0.101 nm and force constant 363171.19999999995 kJ/(nm**2 mol).\n", | ||
| "Bond between 20 and 22 has equilibrium length 0.1335 nm and force constant 410031.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 30 and 24 has equilibrium length 0.1522 nm and force constant 265265.6 kJ/(nm**2 mol).\n", | ||
| "Bond between 30 and 31 has equilibrium length 0.125 nm and force constant 548940.7999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 30 and 32 has equilibrium length 0.125 nm and force constant 548940.7999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 24 and 26 has equilibrium length 0.1526 nm and force constant 259407.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 24 and 25 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 24 and 22 has equilibrium length 0.1449 nm and force constant 282001.5999999999 kJ/(nm**2 mol).\n", | ||
| "Bond between 26 and 27 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 26 and 28 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 26 and 29 has equilibrium length 0.10900000000000001 nm and force constant 284511.99999999994 kJ/(nm**2 mol).\n", | ||
| "Bond between 23 and 22 has equilibrium length 0.101 nm and force constant 363171.19999999995 kJ/(nm**2 mol).\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "for idx in range(harmonic_bond_force.getNumBonds()):\n", | ||
| " idx0, idx1, r0, k = harmonic_bond_force.getBondParameters(idx)\n", | ||
| " print(f\"Bond between {idx0} and {idx1} has equilibrium length {r0} and force constant {k}.\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "9d7dbc26", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "- angles:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 10, | ||
| "id": "fa82f562", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Angle among 0, 4, and 5 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 0, 4, and 6 has equilibrium angle 1.9408061282176945 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 0, 4, and 10 has equilibrium angle 1.9408061282176945 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 1, 0, and 2 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 1, 0, and 3 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 1, 0, and 4 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 2, 0, and 3 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 2, 0, and 4 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 3, 0, and 4 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 4, 6, and 7 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 4, 6, and 8 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 4, 6, and 9 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 4, 10, and 11 has equilibrium angle 2.101376419401173 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 4, 10, and 12 has equilibrium angle 2.035053907825388 rad and force constant 585.76 kJ/(mol rad**2).\n", | ||
| "Angle among 5, 4, and 6 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 5, 4, and 10 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 6, 4, and 10 has equilibrium angle 1.9390607989657 rad and force constant 527.184 kJ/(mol rad**2).\n", | ||
| "Angle among 7, 6, and 8 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 7, 6, and 9 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 8, 6, and 9 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 10, 12, and 13 has equilibrium angle 2.0943951023931953 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 10, 12, and 14 has equilibrium angle 2.1275563581810877 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 11, 10, and 12 has equilibrium angle 2.1450096507010312 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 12, 14, and 15 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 12, 14, and 16 has equilibrium angle 1.9146261894377796 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 12, 14, and 20 has equilibrium angle 1.9216075064457567 rad and force constant 527.184 kJ/(mol rad**2).\n", | ||
| "Angle among 13, 12, and 14 has equilibrium angle 2.0601866490541068 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 14, 16, and 17 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 14, 16, and 18 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 14, 16, and 19 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 14, 20, and 21 has equilibrium angle 2.101376419401173 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 14, 20, and 22 has equilibrium angle 2.035053907825388 rad and force constant 585.76 kJ/(mol rad**2).\n", | ||
| "Angle among 15, 14, and 16 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 15, 14, and 20 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 16, 14, and 20 has equilibrium angle 1.9390607989657 rad and force constant 527.184 kJ/(mol rad**2).\n", | ||
| "Angle among 17, 16, and 18 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 17, 16, and 19 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 18, 16, and 19 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 20, 22, and 23 has equilibrium angle 2.0943951023931953 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 20, 22, and 24 has equilibrium angle 2.1275563581810877 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 21, 20, and 22 has equilibrium angle 2.1450096507010312 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 22, 24, and 25 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 22, 24, and 26 has equilibrium angle 1.9146261894377796 rad and force constant 669.44 kJ/(mol rad**2).\n", | ||
| "Angle among 22, 24, and 30 has equilibrium angle 1.9216075064457567 rad and force constant 527.184 kJ/(mol rad**2).\n", | ||
| "Angle among 23, 22, and 24 has equilibrium angle 2.0601866490541068 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 24, 26, and 27 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 24, 26, and 28 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 24, 26, and 29 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 24, 30, and 31 has equilibrium angle 2.0420352248333655 rad and force constant 585.76 kJ/(mol rad**2).\n", | ||
| "Angle among 24, 30, and 32 has equilibrium angle 2.0420352248333655 rad and force constant 585.76 kJ/(mol rad**2).\n", | ||
| "Angle among 25, 24, and 26 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 25, 24, and 30 has equilibrium angle 1.911135530933791 rad and force constant 418.40000000000003 kJ/(mol rad**2).\n", | ||
| "Angle among 26, 24, and 30 has equilibrium angle 1.9390607989657 rad and force constant 527.184 kJ/(mol rad**2).\n", | ||
| "Angle among 27, 26, and 28 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 27, 26, and 29 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 28, 26, and 29 has equilibrium angle 1.911135530933791 rad and force constant 292.88 kJ/(mol rad**2).\n", | ||
| "Angle among 31, 30, and 32 has equilibrium angle 2.199114857512855 rad and force constant 669.44 kJ/(mol rad**2).\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "for idx in range(harmonic_angle_force.getNumAngles()):\n", | ||
| " idx0, idx1, idx2, r0, k = harmonic_angle_force.getAngleParameters(idx)\n", | ||
| " print(f\"Angle among {idx0}, {idx1}, and {idx2} has equilibrium angle {r0} and force constant {k}.\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "01e07231", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Interestingly, one can also modify such parameters in-place.\n", | ||
| "In a machine learning framework, usually such modification is done gloabally.\n", | ||
| "We here only show how to modify a few bonds and angles, whereas global re-parametrization can be easily achieved in a similar manner with a larger `PyTree` holding all parameters." | ||
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|
||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "ca4e40f9", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Say we would want to modify the bond parameters of the bond between atom 0 and 1." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 27, | ||
| "id": "cbdc43ec", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "for idx in range(harmonic_bond_force.getNumBonds()):\n", | ||
| " idx0, idx1, r0, k = harmonic_bond_force.getBondParameters(idx)\n", | ||
| " if idx0 == 1 and idx1 == 0:\n", | ||
| " new_r0 = unit.Quantity(2666, unit.nanometer)\n", | ||
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|
||
| " new_k = unit.Quantity(1984, unit.kilojoule / (unit.nanometer ** 2 * unit.mole))\n", | ||
| " harmonic_bond_force.setBondParameters(idx, idx0, idx1, new_r0, new_k)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "bb0f5768", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now if you query again you will see that the bond parameter has been changed." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "723167ec", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Similarly, for angles:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 34, | ||
| "id": "e2417613", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "for idx in range(harmonic_angle_force.getNumAngles()):\n", | ||
| " idx0, idx1, idx2, r0, k = harmonic_angle_force.getAngleParameters(idx)\n", | ||
| " if idx0 == 1 and idx1 == 0 and idx2 == 2: \n", | ||
| " new_r0 = unit.Quantity(2666, unit.radian)\n", | ||
| " new_k = unit.Quantity(1984, unit.kilojoule / (unit.radian ** 2 * unit.mole))\n", | ||
| " harmonic_angle_force.setAngleParameters(idx, idx0, idx1, idx2, new_r0, new_k)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "3c2f89e5", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Note that we can use the `unit` module to control the units of the parameters." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "222d4f49", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.3" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } | ||
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This description is overly specific. Nothing in this notebook is really specific to machine learning. You're just showing how to examine and change the parameters in a System. How about something like this?