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Unverified Commit f0bbea98 authored by Alex Izvorski's avatar Alex Izvorski Committed by GitHub
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Add OPC and OPC3 ion sets (#3819) 

* copy opc ions and opc*standard.xml from https://github.com/openmm/openmmforcefields/commit/b12c2e871b60275a10b3f8f56dfc2f6d5447591f

* auto-merged files

* move charges to residue definition

* remove unmerged files

* add docs

* rename U to U4+

* rename Ag+, Tl+, Gd3+ and I- residue names

* fix O-H bond length typo

* add opc3 constraints test
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docs-source/usersguide/application/02_running_sims.rst
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...@@ -505,6 +505,8 @@ File Parameters ...@@ -505,6 +505,8 @@ File Parameters
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions :file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions :file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ============================================ =================================== ============================================
As a convenience, the file :file:`amber14-all.xml` can be used as a shortcut to include As a convenience, the file :file:`amber14-all.xml` can be used as a shortcut to include
......
wrappers/python/openmm/app/data/amber14/opc.xml 0 → 100644
View file @ f0bbea98
<ForceField>
<Info>
<Reference>Izadi S, Anandakrishnan R, Onufriev AV. Building Water Models: A Different Approach. The Journal of Physical Chemistry Letters. 2014 Nov 6;5(21):3863-71. DOI:10.1021/jz501780a</Reference>
<!-- Li/Merz ion parameters of atomic ions for the OPC water model (12-6 set) -->
<DateGenerated>2022-09-28T04:59:42.378081</DateGenerated>
<Source Source="parm/frcmod.ionslm_126_opc" md5hash="61ee47ec99a7ebf66cf09e899a8f0581" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">parm/frcmod.ionslm_126_opc</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">lib/atomic_ions.lib</Source>
</Info>
<AtomTypes>
<Type name="opc-O" class="OW" element="O" mass="16.00000"/>
<Type name="opc-H" class="HW" element="H" mass="1.00800"/>
<Type name="opc-M" class="MW" mass="0"/>
<Type class="ionslm_126_opc-Li+" element="Li" mass="6.94" name="ionslm_126_opc-Li+"/>
<Type class="ionslm_126_opc-Na+" element="Na" mass="22.99" name="ionslm_126_opc-Na+"/>
<Type class="ionslm_126_opc-K+" element="K" mass="39.10" name="ionslm_126_opc-K+"/>
<Type class="ionslm_126_opc-Rb+" element="Rb" mass="85.47" name="ionslm_126_opc-Rb+"/>
<Type class="ionslm_126_opc-Cs+" element="Cs" mass="132.91" name="ionslm_126_opc-Cs+"/>
<Type class="ionslm_126_opc-Tl+" element="Tl" mass="204.38" name="ionslm_126_opc-Tl+"/>
<Type class="ionslm_126_opc-Cu+" element="Cu" mass="63.55" name="ionslm_126_opc-Cu+"/>
<Type class="ionslm_126_opc-Ag+" element="Ag" mass="107.87" name="ionslm_126_opc-Ag+"/>
<Type class="ionslm_126_opc-F-" element="F" mass="19.00" name="ionslm_126_opc-F-"/>
<Type class="ionslm_126_opc-Cl-" element="Cl" mass="35.45" name="ionslm_126_opc-Cl-"/>
<Type class="ionslm_126_opc-Br-" element="Br" mass="79.90" name="ionslm_126_opc-Br-"/>
<Type class="ionslm_126_opc-I-" element="I" mass="126.9" name="ionslm_126_opc-I-"/>
<Type class="ionslm_126_opc-Be2+" element="Be" mass="9.01" name="ionslm_126_opc-Be2+"/>
<Type class="ionslm_126_opc-Cu2+" element="Cu" mass="63.55" name="ionslm_126_opc-Cu2+"/>
<Type class="ionslm_126_opc-Ni2+" element="Ni" mass="58.69" name="ionslm_126_opc-Ni2+"/>
<Type class="ionslm_126_opc-Pt2+" element="Pt" mass="195.08" name="ionslm_126_opc-Pt2+"/>
<Type class="ionslm_126_opc-Zn2+" element="Zn" mass="65.4" name="ionslm_126_opc-Zn2+"/>
<Type class="ionslm_126_opc-Co2+" element="Co" mass="58.93" name="ionslm_126_opc-Co2+"/>
<Type class="ionslm_126_opc-Pd2+" element="Pd" mass="106.42" name="ionslm_126_opc-Pd2+"/>
<Type class="ionslm_126_opc-Ag2+" element="Ag" mass="107.87" name="ionslm_126_opc-Ag2+"/>
<Type class="ionslm_126_opc-Cr2+" element="Cr" mass="52.00" name="ionslm_126_opc-Cr2+"/>
<Type class="ionslm_126_opc-Fe2+" element="Fe" mass="55.85" name="ionslm_126_opc-Fe2+"/>
<Type class="ionslm_126_opc-Mg2+" element="Mg" mass="24.305" name="ionslm_126_opc-Mg2+"/>
<Type class="ionslm_126_opc-V2+" element="V" mass="50.94" name="ionslm_126_opc-V2+"/>
<Type class="ionslm_126_opc-Mn2+" element="Mn" mass="54.94" name="ionslm_126_opc-Mn2+"/>
<Type class="ionslm_126_opc-Hg2+" element="Hg" mass="200.59" name="ionslm_126_opc-Hg2+"/>
<Type class="ionslm_126_opc-Cd2+" element="Cd" mass="112.41" name="ionslm_126_opc-Cd2+"/>
<Type class="ionslm_126_opc-Yb2+" element="Yb" mass="173.05" name="ionslm_126_opc-Yb2+"/>
<Type class="ionslm_126_opc-Ca2+" element="Ca" mass="40.08" name="ionslm_126_opc-Ca2+"/>
<Type class="ionslm_126_opc-Sn2+" element="Sn" mass="118.71" name="ionslm_126_opc-Sn2+"/>
<Type class="ionslm_126_opc-Pb2+" element="Pb" mass="207.2" name="ionslm_126_opc-Pb2+"/>
<Type class="ionslm_126_opc-Eu2+" element="Eu" mass="151.96" name="ionslm_126_opc-Eu2+"/>
<Type class="ionslm_126_opc-Sr2+" element="Sr" mass="87.62" name="ionslm_126_opc-Sr2+"/>
<Type class="ionslm_126_opc-Sm2+" element="Sm" mass="150.36" name="ionslm_126_opc-Sm2+"/>
<Type class="ionslm_126_opc-Ba2+" element="Ba" mass="137.33" name="ionslm_126_opc-Ba2+"/>
<Type class="ionslm_126_opc-Ra2+" element="Ra" mass="226.03" name="ionslm_126_opc-Ra2+"/>
<Type class="ionslm_126_opc-Al3+" element="Al" mass="26.98" name="ionslm_126_opc-Al3+"/>
<Type class="ionslm_126_opc-Fe3+" element="Fe" mass="55.85" name="ionslm_126_opc-Fe3+"/>
<Type class="ionslm_126_opc-Cr3+" element="Cr" mass="52.00" name="ionslm_126_opc-Cr3+"/>
<Type class="ionslm_126_opc-In3+" element="In" mass="114.82" name="ionslm_126_opc-In3+"/>
<Type class="ionslm_126_opc-Tl3+" element="Tl" mass="204.38" name="ionslm_126_opc-Tl3+"/>
<Type class="ionslm_126_opc-Y3+" element="Y" mass="88.91" name="ionslm_126_opc-Y3+"/>
<Type class="ionslm_126_opc-La3+" element="La" mass="138.91" name="ionslm_126_opc-La3+"/>
<Type class="ionslm_126_opc-Ce3+" element="Ce" mass="140.12" name="ionslm_126_opc-Ce3+"/>
<Type class="ionslm_126_opc-Pr3+" element="Pr" mass="140.91" name="ionslm_126_opc-Pr3+"/>
<Type class="ionslm_126_opc-Nd3+" element="Nd" mass="144.24" name="ionslm_126_opc-Nd3+"/>
<Type class="ionslm_126_opc-Sm3+" element="Sm" mass="150.36" name="ionslm_126_opc-Sm3+"/>
<Type class="ionslm_126_opc-Eu3+" element="Eu" mass="151.96" name="ionslm_126_opc-Eu3+"/>
<Type class="ionslm_126_opc-Gd3+" element="Gd" mass="157.25" name="ionslm_126_opc-Gd3+"/>
<Type class="ionslm_126_opc-Tb3+" element="Tb" mass="158.93" name="ionslm_126_opc-Tb3+"/>
<Type class="ionslm_126_opc-Dy3+" element="Dy" mass="162.5" name="ionslm_126_opc-Dy3+"/>
<Type class="ionslm_126_opc-Er3+" element="Er" mass="167.26" name="ionslm_126_opc-Er3+"/>
<Type class="ionslm_126_opc-Tm3+" element="Tm" mass="168.93" name="ionslm_126_opc-Tm3+"/>
<Type class="ionslm_126_opc-Lu3+" element="Lu" mass="174.97" name="ionslm_126_opc-Lu3+"/>
<Type class="ionslm_126_opc-Hf4+" element="Hf" mass="178.49" name="ionslm_126_opc-Hf4+"/>
<Type class="ionslm_126_opc-Zr4+" element="Zr" mass="91.22" name="ionslm_126_opc-Zr4+"/>
<Type class="ionslm_126_opc-Ce4+" element="Ce" mass="140.12" name="ionslm_126_opc-Ce4+"/>
<Type class="ionslm_126_opc-U4+" element="U" mass="238.03" name="ionslm_126_opc-U4+"/>
<Type class="ionslm_126_opc-Pu4+" element="Pu" mass="244.06" name="ionslm_126_opc-Pu4+"/>
<Type class="ionslm_126_opc-Th4+" element="Th" mass="232.04" name="ionslm_126_opc-Th4+"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="O" type="opc-O" charge="0"/>
<Atom name="H1" type="opc-H" charge="0.679142"/>
<Atom name="H2" type="opc-H" charge="0.679142"/>
<Atom name="M" type="opc-M" charge="-1.358284"/>
<!-- weight2 = 0.15939833/(2*(cos(angle/2) * 0.87243313)) -->
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.7045587810585758" weight2="0.1477206094707121" weight3="0.1477206094707121"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
</Residue>
<Residue name="AG1">
<Atom charge="1.0" name="AG1" type="ionslm_126_opc-Ag+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="ionslm_126_opc-Ag2+"/>
</Residue>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="ionslm_126_opc-Al3+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="ionslm_126_opc-Ba2+"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="ionslm_126_opc-Be2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="ionslm_126_opc-Br-"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="ionslm_126_opc-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="ionslm_126_opc-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="ionslm_126_opc-Ce3+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="ionslm_126_opc-Ce4+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="ionslm_126_opc-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="ionslm_126_opc-Co2+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="ionslm_126_opc-Cr2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="ionslm_126_opc-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="ionslm_126_opc-Cs+"/>
</Residue>
<Residue name="CU1">
<Atom charge="1.0" name="CU1" type="ionslm_126_opc-Cu+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="ionslm_126_opc-Cu2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="ionslm_126_opc-Dy3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="ionslm_126_opc-Er3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="ionslm_126_opc-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="ionslm_126_opc-Eu3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="ionslm_126_opc-F-"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="ionslm_126_opc-Fe2+"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="ionslm_126_opc-Fe3+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="ionslm_126_opc-Gd3+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="ionslm_126_opc-Hf4+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="ionslm_126_opc-Hg2+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="ionslm_126_opc-I-"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="ionslm_126_opc-In3+"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="ionslm_126_opc-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="ionslm_126_opc-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="ionslm_126_opc-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="ionslm_126_opc-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="ionslm_126_opc-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="ionslm_126_opc-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="ionslm_126_opc-Na+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="ionslm_126_opc-Nd3+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="ionslm_126_opc-Ni2+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="ionslm_126_opc-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="ionslm_126_opc-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="ionslm_126_opc-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="ionslm_126_opc-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="ionslm_126_opc-Pu4+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="ionslm_126_opc-Ra2+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="ionslm_126_opc-Rb+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="ionslm_126_opc-Sm2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="ionslm_126_opc-Sm3+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="ionslm_126_opc-Sn2+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="ionslm_126_opc-Sr2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="ionslm_126_opc-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="ionslm_126_opc-Th4+"/>
</Residue>
<Residue name="TL1">
<Atom charge="1.0" name="TL1" type="ionslm_126_opc-Tl+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="ionslm_126_opc-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="ionslm_126_opc-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="ionslm_126_opc-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="ionslm_126_opc-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="ionslm_126_opc-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="ionslm_126_opc-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="ionslm_126_opc-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="ionslm_126_opc-Zr4+"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.087243313" k="502416.0"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- angle = arccos(1 - (1.37120510**2 / (2*0.87243313**2))) -->
<Angle class1="HW" class2="OW" class3="HW" angle="1.8081424254418306" k="628.02"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<!-- sigma = (1.777167268 * 2 / (2**(1/6)))*unit.angstrom/unit.nanometer -->
<!-- epsilon = (0.2128008130*unit.kilocalorie)/(unit.kilojoule) -->
<Atom type="opc-O" sigma="0.3166552081964338" epsilon="0.8903586015920001"/>
<Atom type="opc-H" sigma="0.08908987181403394" epsilon="0"/>
<Atom type="opc-M" sigma="0.08908987181403394" epsilon="0"/>
<Atom epsilon="0.009039866720000001" sigma="0.2212992415860603" type="ionslm_126_opc-Li+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.12386075112" sigma="0.2613896839023756" type="ionslm_126_opc-Na+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.58382766144" sigma="0.3032619236549715" type="ionslm_126_opc-K+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.9537620464000001" sigma="0.3239307739158274" type="ionslm_126_opc-Rb+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Cs+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.47070573208000005" sigma="0.29577837442259264" type="ionslm_126_opc-Tl+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.0032724319200000004" sigma="0.21025209748112006" type="ionslm_126_opc-Cu+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.025210566480000002" sigma="0.23448454261453733" type="ionslm_126_opc-Ag+"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.0313754556" sigma="0.3278507282756449" type="ionslm_126_opc-F-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.8400519208" sigma="0.4205041949622401" type="ionslm_126_opc-Cl-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.17863094952" sigma="0.4452711793265416" type="ionslm_126_opc-Br-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.77817463544" sigma="0.5167212565213968" type="ionslm_126_opc-I-"/><!-- HFE set for the OPC water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="5.35552e-06" sigma="0.16410354388145051" type="ionslm_126_opc-Be2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0031585016" sigma="0.20989573799386393" type="ionslm_126_opc-Cu2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00439211216" sigma="0.21328115312279727" type="ionslm_126_opc-Ni2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00631378152" sigma="0.21720110748261476" type="ionslm_126_opc-Pt2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.00631378152" sigma="0.21720110748261476" type="ionslm_126_opc-Zn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.012329536720000001" sigma="0.2250410162022497" type="ionslm_126_opc-Co2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.013433485120000001" sigma="0.2261100946640181" type="ionslm_126_opc-Pd2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="ionslm_126_opc-Ag2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.025210566480000002" sigma="0.23448454261453733" type="ionslm_126_opc-Cr2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="ionslm_126_opc-Fe2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0299963512" sigma="0.23697905902533029" type="ionslm_126_opc-Mg2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.03148911872" sigma="0.23769177799984254" type="ionslm_126_opc-V2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.053825486400000004" sigma="0.2460662259503617" type="ionslm_126_opc-Mn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.053825486400000004" sigma="0.2460662259503617" type="ionslm_126_opc-Hg2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.05861307024" sigma="0.24749166389938626" type="ionslm_126_opc-Cd2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="ionslm_126_opc-Yb2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc-Ca2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="ionslm_126_opc-Sn2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="ionslm_126_opc-Pb2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.73715046696" sigma="0.312349090580003" type="ionslm_126_opc-Eu2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="ionslm_126_opc-Sr2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="ionslm_126_opc-Sm2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Ba2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.47731805816" sigma="0.349232297511013" type="ionslm_126_opc-Ra2+"/><!-- CM set for the OPC water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.010193772080000002" sigma="0.22272467953508485" type="ionslm_126_opc-Al3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.06572013816000001" sigma="0.249451641079295" type="ionslm_126_opc-Fe3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="ionslm_126_opc-Cr3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.09715545064" sigma="0.2565788308244177" type="ionslm_126_opc-In3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="ionslm_126_opc-Tl3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Y3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5781589690400001" sigma="0.30290556416771536" type="ionslm_126_opc-La3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.65093680392" sigma="0.30736005775841707" type="ionslm_126_opc-Ce3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.62720034432" sigma="0.30593461980939257" type="ionslm_126_opc-Pr3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.47580293192" sigma="0.29613473390984874" type="ionslm_126_opc-Nd3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.41662062848000003" sigma="0.2918584200627751" type="ionslm_126_opc-Sm3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.43586389048" sigma="0.2932838580117997" type="ionslm_126_opc-Eu3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc-Gd3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc-Tb3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.29778189072" sigma="0.2820585341632314" type="ionslm_126_opc-Dy3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Er3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.28247819944" sigma="0.2806330962142069" type="ionslm_126_opc-Tm3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.25163082264000003" sigma="0.27760404057252974" type="ionslm_126_opc-Lu3+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.11751709584" sigma="0.26032060544060714" type="ionslm_126_opc-Hf4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14799067408" sigma="0.265131458518565" type="ionslm_126_opc-Zr4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5310938643199999" sigma="0.2998765085260382" type="ionslm_126_opc-Ce4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.5310938643199999" sigma="0.2998765085260382" type="ionslm_126_opc-U4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="ionslm_126_opc-Pu4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.58952354984" sigma="0.3036182831422276" type="ionslm_126_opc-Th4+"/><!-- IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342 -->
</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/amber14/opc3.xml 0 → 100644
View file @ f0bbea98
<ForceField>
<Info>
<DateGenerated>2022-06-21</DateGenerated>
<Reference>Izadi S, Onufriev AV. Accuracy limit of rigid 3-point water models. The Journal of Chemical Physics 145, 074501 (2016); DOI:10.1063/1.4960175</Reference>
<!-- Li/Merz ion parameters of atomic ions for the OPC3 water model (12-6 set) -->
<DateGenerated>2022-09-28T04:59:42.433215</DateGenerated>
<Source Source="parm/frcmod.ionslm_126_opc3" md5hash="5764d233aceb45e3c28df84ac16d1085" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">parm/frcmod.ionslm_126_opc3</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="22.0-py38h6177452_1">lib/atomic_ions.lib</Source>
</Info>
<AtomTypes>
<Type name="opc3-O" class="OW" element="O" mass="16.00000"/>
<Type name="opc3-H" class="HW" element="H" mass="1.00800"/>
<Type class="ionslm_126_opc3-Li+" element="Li" mass="6.94" name="ionslm_126_opc3-Li+"/>
<Type class="ionslm_126_opc3-Na+" element="Na" mass="22.99" name="ionslm_126_opc3-Na+"/>
<Type class="ionslm_126_opc3-K+" element="K" mass="39.10" name="ionslm_126_opc3-K+"/>
<Type class="ionslm_126_opc3-Rb+" element="Rb" mass="85.47" name="ionslm_126_opc3-Rb+"/>
<Type class="ionslm_126_opc3-Cs+" element="Cs" mass="132.91" name="ionslm_126_opc3-Cs+"/>
<Type class="ionslm_126_opc3-Tl+" element="Tl" mass="204.38" name="ionslm_126_opc3-Tl+"/>
<Type class="ionslm_126_opc3-Cu+" element="Cu" mass="63.55" name="ionslm_126_opc3-Cu+"/>
<Type class="ionslm_126_opc3-Ag+" element="Ag" mass="107.87" name="ionslm_126_opc3-Ag+"/>
<Type class="ionslm_126_opc3-F-" element="F" mass="19.00" name="ionslm_126_opc3-F-"/>
<Type class="ionslm_126_opc3-Cl-" element="Cl" mass="35.45" name="ionslm_126_opc3-Cl-"/>
<Type class="ionslm_126_opc3-Br-" element="Br" mass="79.90" name="ionslm_126_opc3-Br-"/>
<Type class="ionslm_126_opc3-I-" element="I" mass="126.9" name="ionslm_126_opc3-I-"/>
<Type class="ionslm_126_opc3-Be2+" element="Be" mass="9.01" name="ionslm_126_opc3-Be2+"/>
<Type class="ionslm_126_opc3-Cu2+" element="Cu" mass="63.55" name="ionslm_126_opc3-Cu2+"/>
<Type class="ionslm_126_opc3-Ni2+" element="Ni" mass="58.69" name="ionslm_126_opc3-Ni2+"/>
<Type class="ionslm_126_opc3-Pt2+" element="Pt" mass="195.08" name="ionslm_126_opc3-Pt2+"/>
<Type class="ionslm_126_opc3-Zn2+" element="Zn" mass="65.4" name="ionslm_126_opc3-Zn2+"/>
<Type class="ionslm_126_opc3-Co2+" element="Co" mass="58.93" name="ionslm_126_opc3-Co2+"/>
<Type class="ionslm_126_opc3-Pd2+" element="Pd" mass="106.42" name="ionslm_126_opc3-Pd2+"/>
<Type class="ionslm_126_opc3-Ag2+" element="Ag" mass="107.87" name="ionslm_126_opc3-Ag2+"/>
<Type class="ionslm_126_opc3-Cr2+" element="Cr" mass="52.00" name="ionslm_126_opc3-Cr2+"/>
<Type class="ionslm_126_opc3-Fe2+" element="Fe" mass="55.85" name="ionslm_126_opc3-Fe2+"/>
<Type class="ionslm_126_opc3-Mg2+" element="Mg" mass="24.305" name="ionslm_126_opc3-Mg2+"/>
<Type class="ionslm_126_opc3-V2+" element="V" mass="50.94" name="ionslm_126_opc3-V2+"/>
<Type class="ionslm_126_opc3-Mn2+" element="Mn" mass="54.94" name="ionslm_126_opc3-Mn2+"/>
<Type class="ionslm_126_opc3-Hg2+" element="Hg" mass="200.59" name="ionslm_126_opc3-Hg2+"/>
<Type class="ionslm_126_opc3-Cd2+" element="Cd" mass="112.41" name="ionslm_126_opc3-Cd2+"/>
<Type class="ionslm_126_opc3-Yb2+" element="Yb" mass="173.05" name="ionslm_126_opc3-Yb2+"/>
<Type class="ionslm_126_opc3-Ca2+" element="Ca" mass="40.08" name="ionslm_126_opc3-Ca2+"/>
<Type class="ionslm_126_opc3-Sn2+" element="Sn" mass="118.71" name="ionslm_126_opc3-Sn2+"/>
<Type class="ionslm_126_opc3-Pb2+" element="Pb" mass="207.2" name="ionslm_126_opc3-Pb2+"/>
<Type class="ionslm_126_opc3-Eu2+" element="Eu" mass="151.96" name="ionslm_126_opc3-Eu2+"/>
<Type class="ionslm_126_opc3-Sr2+" element="Sr" mass="87.62" name="ionslm_126_opc3-Sr2+"/>
<Type class="ionslm_126_opc3-Sm2+" element="Sm" mass="150.36" name="ionslm_126_opc3-Sm2+"/>
<Type class="ionslm_126_opc3-Ba2+" element="Ba" mass="137.33" name="ionslm_126_opc3-Ba2+"/>
<Type class="ionslm_126_opc3-Ra2+" element="Ra" mass="226.03" name="ionslm_126_opc3-Ra2+"/>
<Type class="ionslm_126_opc3-Al3+" element="Al" mass="26.98" name="ionslm_126_opc3-Al3+"/>
<Type class="ionslm_126_opc3-Fe3+" element="Fe" mass="55.85" name="ionslm_126_opc3-Fe3+"/>
<Type class="ionslm_126_opc3-Cr3+" element="Cr" mass="52.00" name="ionslm_126_opc3-Cr3+"/>
<Type class="ionslm_126_opc3-In3+" element="In" mass="114.82" name="ionslm_126_opc3-In3+"/>
<Type class="ionslm_126_opc3-Tl3+" element="Tl" mass="204.38" name="ionslm_126_opc3-Tl3+"/>
<Type class="ionslm_126_opc3-Y3+" element="Y" mass="88.91" name="ionslm_126_opc3-Y3+"/>
<Type class="ionslm_126_opc3-La3+" element="La" mass="138.91" name="ionslm_126_opc3-La3+"/>
<Type class="ionslm_126_opc3-Ce3+" element="Ce" mass="140.12" name="ionslm_126_opc3-Ce3+"/>
<Type class="ionslm_126_opc3-Pr3+" element="Pr" mass="140.91" name="ionslm_126_opc3-Pr3+"/>
<Type class="ionslm_126_opc3-Nd3+" element="Nd" mass="144.24" name="ionslm_126_opc3-Nd3+"/>
<Type class="ionslm_126_opc3-Sm3+" element="Sm" mass="150.36" name="ionslm_126_opc3-Sm3+"/>
<Type class="ionslm_126_opc3-Eu3+" element="Eu" mass="151.96" name="ionslm_126_opc3-Eu3+"/>
<Type class="ionslm_126_opc3-Gd3+" element="Gd" mass="157.25" name="ionslm_126_opc3-Gd3+"/>
<Type class="ionslm_126_opc3-Tb3+" element="Tb" mass="158.93" name="ionslm_126_opc3-Tb3+"/>
<Type class="ionslm_126_opc3-Dy3+" element="Dy" mass="162.5" name="ionslm_126_opc3-Dy3+"/>
<Type class="ionslm_126_opc3-Er3+" element="Er" mass="167.26" name="ionslm_126_opc3-Er3+"/>
<Type class="ionslm_126_opc3-Tm3+" element="Tm" mass="168.93" name="ionslm_126_opc3-Tm3+"/>
<Type class="ionslm_126_opc3-Lu3+" element="Lu" mass="174.97" name="ionslm_126_opc3-Lu3+"/>
<Type class="ionslm_126_opc3-Hf4+" element="Hf" mass="178.49" name="ionslm_126_opc3-Hf4+"/>
<Type class="ionslm_126_opc3-Zr4+" element="Zr" mass="91.22" name="ionslm_126_opc3-Zr4+"/>
<Type class="ionslm_126_opc3-Ce4+" element="Ce" mass="140.12" name="ionslm_126_opc3-Ce4+"/>
<Type class="ionslm_126_opc3-U4+" element="U" mass="238.03" name="ionslm_126_opc3-U4+"/>
<Type class="ionslm_126_opc3-Pu4+" element="Pu" mass="244.06" name="ionslm_126_opc3-Pu4+"/>
<Type class="ionslm_126_opc3-Th4+" element="Th" mass="232.04" name="ionslm_126_opc3-Th4+"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="O" type="opc3-O" charge="-0.895170"/>
<Atom name="H1" type="opc3-H" charge="0.447585"/>
<Atom name="H2" type="opc3-H" charge="0.447585"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
<Residue name="AG1">
<Atom charge="1.0" name="AG1" type="ionslm_126_opc3-Ag+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="ionslm_126_opc3-Ag2+"/>
</Residue>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="ionslm_126_opc3-Al3+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="ionslm_126_opc3-Ba2+"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="ionslm_126_opc3-Be2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="ionslm_126_opc3-Br-"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="ionslm_126_opc3-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="ionslm_126_opc3-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="ionslm_126_opc3-Ce3+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="ionslm_126_opc3-Ce4+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="ionslm_126_opc3-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="ionslm_126_opc3-Co2+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="ionslm_126_opc3-Cr2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="ionslm_126_opc3-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="ionslm_126_opc3-Cs+"/>
</Residue>
<Residue name="CU1">
<Atom charge="1.0" name="CU1" type="ionslm_126_opc3-Cu+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="ionslm_126_opc3-Cu2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="ionslm_126_opc3-Dy3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="ionslm_126_opc3-Er3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="ionslm_126_opc3-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="ionslm_126_opc3-Eu3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="ionslm_126_opc3-F-"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="ionslm_126_opc3-Fe2+"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="ionslm_126_opc3-Fe3+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="ionslm_126_opc3-Gd3+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="ionslm_126_opc3-Hf4+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="ionslm_126_opc3-Hg2+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="ionslm_126_opc3-I-"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="ionslm_126_opc3-In3+"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="ionslm_126_opc3-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="ionslm_126_opc3-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="ionslm_126_opc3-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="ionslm_126_opc3-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="ionslm_126_opc3-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="ionslm_126_opc3-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="ionslm_126_opc3-Na+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="ionslm_126_opc3-Nd3+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="ionslm_126_opc3-Ni2+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="ionslm_126_opc3-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="ionslm_126_opc3-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="ionslm_126_opc3-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="ionslm_126_opc3-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="ionslm_126_opc3-Pu4+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="ionslm_126_opc3-Ra2+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="ionslm_126_opc3-Rb+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="ionslm_126_opc3-Sm2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="ionslm_126_opc3-Sm3+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="ionslm_126_opc3-Sn2+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="ionslm_126_opc3-Sr2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="ionslm_126_opc3-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="ionslm_126_opc3-Th4+"/>
</Residue>
<Residue name="TL1">
<Atom charge="1.0" name="TL1" type="ionslm_126_opc3-Tl+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="ionslm_126_opc3-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="ionslm_126_opc3-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="ionslm_126_opc3-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="ionslm_126_opc3-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="ionslm_126_opc3-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="ionslm_126_opc3-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="ionslm_126_opc3-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="ionslm_126_opc3-Zr4+"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.0978882" k="502416.0"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) -->
<Angle class1="HW" class2="OW" class3="HW" angle="1.9106321528999624" k="628.02"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<!-- sigma = (1.7814990 * 2 / (2**(1/6)))*unit.angstrom/unit.nanometer -->
<!-- epsilon = (0.163406*unit.kilocalorie)/(unit.kilojoule) -->
<Atom type="opc3-O" sigma="0.31742703509365927" epsilon="0.683690704"/>
<Atom type="opc3-H" sigma="1" epsilon="0"/>
<Atom epsilon="0.013625196" sigma="0.22628827440764618" type="ionslm_126_opc3-Li+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.1260287744" sigma="0.2617460433896317" type="ionslm_126_opc3-Na+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.58667223752" sigma="0.3034401033985996" type="ionslm_126_opc3-K+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.89173069" sigma="0.32072353853052216" type="ionslm_126_opc3-Rb+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="1.4963237108" sigma="0.35012319622915333" type="ionslm_126_opc3-Cs+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.52838869912" sigma="0.29969832878241015" type="ionslm_126_opc3-Tl+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.004698632" sigma="0.2139938720973095" type="ionslm_126_opc3-Cu+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.0318714108" sigma="0.2378699577434706" type="ionslm_126_opc3-Ag+"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="0.9537620464000001" sigma="0.3239307739158274" type="ionslm_126_opc3-F-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.68724395648" sigma="0.4108824888063245" type="ionslm_126_opc3-Cl-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.18294026032" sigma="0.4456275388137977" type="ionslm_126_opc3-Br-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="3.64743605776" sigma="0.4953396872860286" type="ionslm_126_opc3-I-"/><!-- HFE set for the OPC3 water model from Sengupta et al., JCIM, 2021, 61, 869 -->
<Atom epsilon="2.598264e-05" sigma="0.17301253106285389" type="ionslm_126_opc3-Be2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.007283507200000001" sigma="0.2188047251752673" type="ionslm_126_opc3-Cu2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="ionslm_126_opc3-Ni2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.014015354" sigma="0.22664463389490233" type="ionslm_126_opc3-Pt2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.015669289200000002" sigma="0.22807007184392686" type="ionslm_126_opc3-Zn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.022184153760000002" sigma="0.23270274517825662" type="ionslm_126_opc3-Co2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0230594884" sigma="0.23323728440914082" type="ionslm_126_opc3-Pd2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.033437523840000004" sigma="0.23858267671798283" type="ionslm_126_opc3-Ag2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.03762051968" sigma="0.24036447415426354" type="ionslm_126_opc3-Cr2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.04078617592000001" sigma="0.24161173235966005" type="ionslm_126_opc3-Fe2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.04415701552" sigma="0.2428589905650565" type="ionslm_126_opc3-Mg2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.045666519040000006" sigma="0.2433935297959407" type="ionslm_126_opc3-V2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0727321456" sigma="0.25123343851557567" type="ionslm_126_opc3-Mn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.0727321456" sigma="0.25123343851557567" type="ionslm_126_opc3-Hg2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.07494179968" sigma="0.25176797774645987" type="ionslm_126_opc3-Cd2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.37961047072000004" sigma="0.2890075441647261" type="ionslm_126_opc3-Yb2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.39325717248000003" sigma="0.2900766226264945" type="ionslm_126_opc3-Ca2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.423779578" sigma="0.2923929592936593" type="ionslm_126_opc3-Sn2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.64496410208" sigma="0.307003698271161" type="ionslm_126_opc3-Pb2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.7982505068" sigma="0.31573450570893624" type="ionslm_126_opc3-Eu2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.8179506616000001" sigma="0.31680358417070464" type="ionslm_126_opc3-Sr2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.8378363768" sigma="0.31787266263247305" type="ionslm_126_opc3-Sm2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.5001257116000002" sigma="0.35030137597278144" type="ionslm_126_opc3-Ba2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="1.5001257116000002" sigma="0.35030137597278144" type="ionslm_126_opc3-Ra2+"/><!-- CM set for the OPC3 water model from Li et al., JCTC, 2020, 16, 4429 -->
<Atom epsilon="0.01724489992" sigma="0.22931733004932334" type="ionslm_126_opc3-Al3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.07951189920000001" sigma="0.2528370562082283" type="ionslm_126_opc3-Fe3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="ionslm_126_opc3-Cr3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.10942737368000001" sigma="0.25889516749158265" type="ionslm_126_opc3-In3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.15799491096" sigma="0.2665568964675895" type="ionslm_126_opc3-Tl3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Y3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.67508049224" sigma="0.3087854957074416" type="ionslm_126_opc3-La3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="ionslm_126_opc3-Ce3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.7276888530400001" sigma="0.3118145513491188" type="ionslm_126_opc3-Pr3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.55575929744" sigma="0.3014801262186908" type="ionslm_126_opc3-Nd3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="ionslm_126_opc3-Sm3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.50965295632" sigma="0.2984510705770137" type="ionslm_126_opc3-Eu3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="ionslm_126_opc3-Gd3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.40484250112000003" sigma="0.2909675213446348" type="ionslm_126_opc3-Tb3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.34886028824000004" sigma="0.2865130277539331" type="ionslm_126_opc3-Dy3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Er3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="ionslm_126_opc3-Tm3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.29778189072" sigma="0.2820585341632314" type="ionslm_126_opc3-Lu3+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.14921629320000002" sigma="0.26530963826219306" type="ionslm_126_opc3-Hf4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.17386691496" sigma="0.2686950533911263" type="ionslm_126_opc3-Zr4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.6009964544" sigma="0.3043310021167399" type="ionslm_126_opc3-Ce4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.6009964544" sigma="0.3043310021167399" type="ionslm_126_opc3-U4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.52838869912" sigma="0.29969832878241015" type="ionslm_126_opc3-Pu4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
<Atom epsilon="0.63901700632" sigma="0.3066473387839048" type="ionslm_126_opc3-Th4+"/><!-- IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342 -->
</NonbondedForce>
</ForceField>
wrappers/python/openmm/app/data/opc3.xml
View file @ f0bbea98
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
</Residue> </Residue>
</Residues> </Residues>
<HarmonicBondForce> <HarmonicBondForce>
<Bond class1="OW" class2="HW" length="0.978882" k="502416.0"/> <Bond class1="OW" class2="HW" length="0.0978882" k="502416.0"/>
</HarmonicBondForce> </HarmonicBondForce>
<HarmonicAngleForce> <HarmonicAngleForce>
<!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) --> <!-- angle = arccos(1 - (1.598507**2 / (2*0.978882**2))) -->
......
wrappers/python/tests/TestForceField.py
View file @ f0bbea98
...@@ -1325,6 +1325,13 @@ self.scriptExecuted = True ...@@ -1325,6 +1325,13 @@ self.scriptExecuted = True
# -2532.4862082354407 # -2532.4862082354407
self.assertTrue(abs(energy1 - energy_amber) < energy_tolerance) self.assertTrue(abs(energy1 - energy_amber) < energy_tolerance)
context.applyConstraints(1e-12)
state = context.getState(getEnergy=True)
energy2 = state.getPotentialEnergy().value_in_unit(kilocalorie_per_mole)
self.assertTrue(abs(energy1 - energy_amber) < energy_tolerance)
self.assertTrue(abs(energy1 - energy2) < energy_tolerance)
class AmoebaTestForceField(unittest.TestCase): class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield.""" """Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......
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