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Not only querying, but also modifying system parameters #18

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merged 14 commits into from
May 1, 2023
Merged

Not only querying, but also modifying system parameters #18

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6a01959
Modifying parameter
yuanqing-wang Apr 19, 2023
e7b035c
title change
yuanqing-wang Apr 19, 2023
4266d19
start implementing own functional forms
yuanqing-wang Apr 19, 2023
5681941
get energy components
yuanqing-wang Apr 19, 2023
a052c97
trash clean
yuanqing-wang Apr 19, 2023
c938c42
Merge branch 'main' of https://github.com/yuanqing-wang/openmm-cookbook
yuanqing-wang Apr 19, 2023
7c6d594
Update Use OpenMM to Verify Your MM Functional Form Implementation.ipynb
yuanqing-wang Apr 19, 2023
08af908
trash cleaning
yuanqing-wang Apr 19, 2023
38035e4
merged modifying parameters into querying parameters
yuanqing-wang Apr 20, 2023
9c47ba7
moved benchmarking script into another PR; fixed typo; added querying…
yuanqing-wang Apr 25, 2023
d385b96
Merge branch 'openmm:main' into main
yuanqing-wang Apr 25, 2023
f821029
minor fixes; update parameters in `Context`
yuanqing-wang Apr 26, 2023
eafe1df
remove line char limit; get rid of `Context`
yuanqing-wang Apr 28, 2023
4c9438a
removed redundant line
yuanqing-wang May 1, 2023
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131 changes: 122 additions & 9 deletions ...erying Charges and Other Parameters.ipynb → ...ifying Charges and Other Parameters.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@
"id": "3a4fdeed",
"metadata": {},
"source": [
"## Querying Charges and Other Parameters\n",
"## Querying and Modifying Charges and Other Parameters\n",
"\n",
"Sometimes you want to inspect the charges or other parameters of the particles or bonds in a System. Force field parameters are stored in the Force objects added to a System. As an example, let's load a PDB file and model it using the Amber14 force field."
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"id": "9323aaae",
"metadata": {},
"outputs": [],
Expand All @@ -25,6 +25,28 @@
"system = forcefield.createSystem(pdb.topology)"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "6d26c481",
"metadata": {},
"source": [
"Let's also create a `Simulation` with this system."
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "552481f3",
"metadata": {},
"outputs": [],
"source": [
"integrator = LangevinMiddleIntegrator(\n",
" 300 * unit.kelvin, 1 / unit.picosecond, 0.004 * unit.picoseconds)\n",
"simulation = Simulation(pdb.topology, system, integrator)\n",
"simulation.context.setPositions(pdb.positions)"
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]
},
{
"cell_type": "markdown",
"id": "3c6c73f4",
Expand All @@ -35,7 +57,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 3,
"id": "1734190f",
"metadata": {},
"outputs": [],
Expand All @@ -53,7 +75,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"id": "bf38fc9a",
"metadata": {},
"outputs": [],
Expand All @@ -76,7 +98,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 6,
"id": "933928f9",
"metadata": {},
"outputs": [
Expand All @@ -98,12 +120,98 @@
" if particle1 == 0 or particle2 == 0:\n",
" print(f'Particles ({particle1}, {particle2}), length = {length}, k = {k}')"
]
},
{
"cell_type": "markdown",
"id": "50f5157c",
"metadata": {},
"source": [
"In some cases you may want to modify those parameters to make a bond behave differently from what the `ForceField` assigned.\n",
"We show you here that to modify these parameters are also easy."
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "cd5396c5",
"metadata": {},
"source": [
"Let's say we would want to modify the force constant of the bond connecting particle 1 and 0 to a new number."
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "086c7629",
"metadata": {},
"outputs": [],
"source": [
"for i in range(bonded.getNumBonds()):\n",
" particle1, particle2, length, k = bonded.getBondParameters(i)\n",
" if particle1 == 1 and particle2 == 0:\n",
" bonded.setBondParameters(\n",
" i, particle1, particle2, length, \n",
" 2666 * unit.kilojoules_per_mole/unit.nanometer**2\n",
" )"
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No need to split this onto four lines. It makes the code less readable, and it can easily fit on a single line.

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Sure! If we don't worry about the 80 char limit.

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If someone wants to view the entry on a VT52 terminal, I admit it will be inconvenient. But I think we can say VT100 is the earliest terminal we support. :)

]
},
{
"cell_type": "markdown",
"id": "8f9728ad",
"metadata": {},
"source": [
"Now if you query again you can see new parameters."
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "68498ff5",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Particles (4, 0), length = 0.1471 nm, k = 307105.5999999999 kJ/(nm**2 mol)\n",
"Particles (1, 0), length = 0.101 nm, k = 2666.0 kJ/(nm**2 mol)\n",
"Particles (2, 0), length = 0.101 nm, k = 363171.19999999995 kJ/(nm**2 mol)\n",
"Particles (3, 0), length = 0.101 nm, k = 363171.19999999995 kJ/(nm**2 mol)\n"
]
}
],
"source": [
"bonded = [f for f in system.getForces() if isinstance(f, HarmonicBondForce)][0]\n",
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"for i in range(bonded.getNumBonds()):\n",
" particle1, particle2, length, k = bonded.getBondParameters(i)\n",
" if particle1 == 0 or particle2 == 0:\n",
" print(f'Particles ({particle1}, {particle2}), length = {length}, k = {k}')"
]
},
{
"attachments": {},
"cell_type": "markdown",
"id": "47729e2e",
"metadata": {},
"source": [
"Modifying `Force` objects will affect any new `Simulations` or `Contexts` you create, but it will have no effect on ones that already exist. \n",
"If you want your modifications to apply to an existing `Simulation`, you can copy them over by calling"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "77075eed",
"metadata": {},
"outputs": [],
"source": [
"bonded.updateParametersInContext(simulation.context)"
]
}
],
"metadata": {
"tags": ["force field", "inspection", "forces"],
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -117,8 +225,13 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.1"
}
"version": "3.11.3"
},
"tags": [
"force field",
"inspection",
"forces"
]
},
"nbformat": 4,
"nbformat_minor": 5
Expand Down