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SMIRNOFF: support virtual sites, multiple force field files #423

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8b8c9cc
Support virtual sites and multiple SMIRNOFF force fields
epretti Dec 12, 2025
fbd23bf
Put test files where tests can actually find them
epretti Dec 12, 2025
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120 changes: 120 additions & 0 deletions openmmforcefields/data/test-virtual-sites.offxml
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<?xml version="1.0" encoding="utf-8"?>

<!--
MIT License

Copyright (c) 2020 Open Force Field Initiative

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
-->

<SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
<VirtualSites version="0.3" exclusion_policy="parents">
<!-- A chlorine bound to (any) carbon, for fixing sigma holes -->
<VirtualSite
smirks="[#6:2]-[#17X1:1]"
epsilon="0.0 * kilojoules_per_mole ** 1"
type="BondCharge"
match="all_permutations"
distance="1.45 * angstrom ** 1"
outOfPlaneAngle="None"
inPlaneAngle="None"
charge_increment1="-0.063 * elementary_charge ** 1"
charge_increment2="0.0 * elementary_charge ** 1"
sigma="0.0 * angstrom ** 1"
name="sigma_hole">
</VirtualSite>
<!-- An oxygen in a carbonyl group, flip outOfPlaneAngle to 41 -->
<VirtualSite
smirks="[#8:1]=[#6X3+0:2]-[#6:3]"
epsilon="0.1 * kilocalories_per_mole ** 1"
type="MonovalentLonePair"
match="all_permutations"
distance="0.5 * angstrom ** 1"
outOfPlaneAngle="0 * degree ** 1"
inPlaneAngle="110 * degree ** 1"
charge_increment1="0.1 * elementary_charge ** 1"
charge_increment2="0.0 * elementary_charge ** 1"
charge_increment3="0.0 * elementary_charge ** 1"
sigma="0.05 * angstrom ** 1"
name="planar_carbonyl">
</VirtualSite>
<!-- A conventional four-site water model -->
<VirtualSite
smirks="[#1:2]-[#8X2H2+0:1]-[#1:3]"
epsilon="0.6 * kilojoules_per_mole ** 1"
type="DivalentLonePair"
match="once"
distance="-0.15 * angstrom ** 1"
outOfPlaneAngle="0 * degree ** 1"
inPlaneAngle="None"
charge_increment1="0.0 * elementary_charge ** 1"
charge_increment2="1 * elementary_charge ** 1"
charge_increment3="1 * elementary_charge ** 1"
sigma="0.7 * angstrom ** 1"
name="4_site_water">
</VirtualSite>
<!-- On order to avoid applying two water models at the same time, this file -->
<!-- only includes four-site water parameters. To see a conventional -->
<!-- five-site water model, load ForceField("tip5p.offxml") -->
<!-- -->
<!-- A trivalent nitrogen, occupying the location of the lone pair -->
<!-- 5 nm distance looks comically large - can we do 0.5 or 1 A? -->
<VirtualSite
smirks="[#1:2][#7:1]([#1:3])[#1:4]"
epsilon="0.5 * kilojoules_per_mole ** 1"
type="TrivalentLonePair"
match="once"
distance="0.3 * angstrom ** 1"
outOfPlaneAngle="None"
inPlaneAngle="None"
charge_increment1="0.2 * elementary_charge ** 1"
charge_increment2="0.0 * elementary_charge ** 1"
charge_increment3="0.0 * elementary_charge ** 1"
charge_increment4="0.0 * elementary_charge ** 1"
sigma="1.0 * angstrom ** 1"
name="trivalent_nitrogen">
</VirtualSite>
</VirtualSites>
<Electrostatics version="0.4"
scale12="0.0"
scale13="0.0"
scale14="0.833333"
scale15="1.0"
cutoff="9.0 * angstrom ** 1"
switch_width="0.0 * angstrom ** 1"
periodic_potential="Ewald3D-ConductingBoundary"
nonperiodic_potential="Coulomb"
exception_potential="Coulomb">
</Electrostatics>
<vdW version="0.3"
potential="Lennard-Jones-12-6"
combining_rules="Lorentz-Berthelot"
scale12="0.0"
scale13="0.0"
scale14="0.5"
scale15="1.0"
cutoff="9.0 * angstrom ** 1"
switch_width="1.0 * angstrom ** 1"
method="cutoff">
<Atom smirks="[*:1]"
epsilon="0 * kilojoules_per_mole ** 1" sigma="1.0 * angstrom ** 1">
</Atom>
</vdW>
</SMIRNOFF>
18 changes: 18 additions & 0 deletions openmmforcefields/data/test-water-cluster.pdb
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REMARK 1 CREATED WITH OPENMM 8.4, 2025-12-12
HETATM 1 O HOH A 1 0.193 -1.132 1.359 1.00 0.00 O
HETATM 2 H1 HOH A 1 0.795 -1.298 2.115 1.00 0.00 H
HETATM 3 H2 HOH A 1 0.226 -0.143 1.173 1.00 0.00 H
HETATM 4 O HOH A 2 0.371 1.492 0.846 1.00 0.00 O
HETATM 5 H1 HOH A 2 0.454 1.574 -0.154 1.00 0.00 H
HETATM 6 H2 HOH A 2 0.177 2.390 1.187 1.00 0.00 H
HETATM 7 O HOH A 3 -0.958 -2.171 -0.827 1.00 0.00 O
HETATM 8 H1 HOH A 3 -1.669 -2.759 -0.497 1.00 0.00 H
HETATM 9 H2 HOH A 3 -0.491 -1.799 -0.016 1.00 0.00 H
HETATM 10 O HOH A 4 0.508 1.753 -1.821 1.00 0.00 O
HETATM 11 H1 HOH A 4 0.262 0.851 -2.195 1.00 0.00 H
HETATM 12 H2 HOH A 4 0.730 2.324 -2.586 1.00 0.00 H
HETATM 13 O HOH A 5 -0.117 -0.640 -2.863 1.00 0.00 O
HETATM 14 H1 HOH A 5 -0.030 -1.248 -3.627 1.00 0.00 H
HETATM 15 H2 HOH A 5 -0.452 -1.194 -2.092 1.00 0.00 H
TER 16 HOH A 5
END
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