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OPLSaa_perfluoroalkanes.xml
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OPLSaa_perfluoroalkanes.xml
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<!--
OPLS forcefield for perfluoroalkanes
Source: Watkins and Jorgensen, J. Phys. Chem. A, 105, 2001 pp 4118-4125 DOI:10.1021/jp004071w
Forcefield file initially created on 04 August 2017 by C.R. Iacovella
While all parameters are listed in Watkins and Jorgensen, bond and angle parameters have various original sources, as annotated in the manuscript:
- CT-F Bonds come from reference doi="10.1002/jcc.540130806"
- F-CT-F angles are from reference doi="10.1021/ja00124a002"
- CT-CT-F angles are the same as CT-CT-OH and CT-CT-OS from reference: doi="10.1021/ja00124a002"
- Bonds and angles for the CT-CT and CT-CT-CT are the same as for alkanes from reference, doi="10.1021/ja9621760"
Additional Notes
- These are the "general" parameters for perfluoroalkanes; specific dihedrals exist for 4 and 5-mers
- The backbone dihedral specifically references opls_962 (i.e. C-CF2-C) rather than only using the "CT" class;
if only the "CT" class were used, this would create a conflict with alkane systems if the parameters were merged.
- The original parameters are defined as kcal/mol, this file uses kJ/mol; a conversion factor of 4.184 was used,
consistent with openMM.
- PI is defined as 3.141592653589 for conversion to radians, consistent with openMM.
- Atom type names, e.g., opls_961, correspond to those defined in the OPLS forcefield itp file distributed with GROMACS.
- Conversion from OPLS-style dihedrals to RB follow the formulas detailed in the GROMACS manual. Specifically,
OPLS form:
0.5*(F1*(1+cos(phi))+ F2*(1-cos(2phi))+ F3*(1+cos(3phi))+F4*(1-cos(4phi)))
RB mapping:
c0 = F2+0.5*(F1+F3)
c1 = 0.5*(-F1+3F3)
c2 = -F2 + 4F4
c3 = -2F3
c4 = -4F4
c5 = 0
-->
<ForceField>
<AtomTypes>
<Type name="opls_961" class="CT" element="C" mass="12.01100" def="[C;X4](F)(F)(F)(C)" desc="perfluoroalkane CF3" doi="10.1021/jp004071w"/>
<Type name="opls_962" class="CT" element="C" mass="12.01100" def="[C;X4](F)(F)(C)(C)" desc="perfluoroalkane CF2" doi="10.1021/jp004071w"/>
<Type name="opls_963" class="CT" element="C" mass="12.011" def="[C;X4](F)(C)(C)(C)" desc="perfluoroalkane CF" doi="10.1021/jp004071w"/>
<Type name="opls_964" class="CT" element="C" mass="12.011" def="[C;X4](F)(F)(F)(F)" desc="perfluoroalkane CF4" doi="10.1021/jp004071w"/>
<Type name="opls_965" class="F" element="F" mass="18.9984" def="FC" desc="perfluoroalkane F" doi="10.1021/jp004071w"/>
</AtomTypes>
<HarmonicBondForce>
<Bond class1="CT" class2="CT" length="0.1529" k="224262.4"/> <!--doi="10.1021/ja9621760"-->
<Bond class1="CT" class2="F" length="0.1332" k="307105.6"/> <!--doi="10.1002/jcc.540130806-->
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle class1="CT" class2="CT" class3="CT" angle="1.966986067" k="488.273"/> <!--doi="10.1021/ja9621760"-->
<Angle class1="CT" class2="CT" class3="F" angle="1.91113553093" k="418.4"/> <!--doi="10.1021/ja00124a002"-->
<Angle class1="F" class2="CT" class3="F" angle="1.904154214" k="644.336"/> <!--doi="10.1021/ja00124a002"-->
</HarmonicAngleForce>
<RBTorsionForce>
<Proper class1="CT" type2="opls_962" type3="opls_962" class4="CT" c0="14.91596" c1="-22.564312" c2="-39.41328" c3="11.614784" c4="35.446848" c5="0.0"/> <!--doi="10.1021/jp004071w"-->
<Proper type1="opls_961" type2="opls_963" type3="opls_962" type4="opls_961" c0="15.85736" c1="-19.940944" c2="-27.606032" c3="3.64008" c4="28.049536" c5="0.0"/> <!--doi="10.1021/jp004071w"-->
<Proper class1="F" class2="CT" class3="CT" class4="F" c0="-4.707" c1="6.799" c2="0.0" c3="-2.092" c4="0.0" c5="0.0"/> <!--doi="10.1021/jp004071w"-->
<Proper class1="CT" class2="CT" class3="CT" class4="F" c0="1.4644" c1="1.8828" c2="0.0" c3="-3.3472" c4="0.0" c5="0.0"/> <!--doi="10.1021/jp004071w"-->
</RBTorsionForce>
<NonbondedForce coulomb14scale="0.5" lj14scale="0.5">
<Atom type="opls_961" charge="0.36" sigma="0.35" epsilon="0.276144"/>
<Atom type="opls_962" charge="0.24" sigma="0.35" epsilon="0.276144"/>
<Atom type="opls_963" charge="0.12" sigma="0.35" epsilon="0.276144"/>
<Atom type="opls_964" charge="0.48" sigma="0.35" epsilon="0.405848"/>
<Atom type="opls_965" charge="-0.12" sigma="0.295" epsilon="0.221752"/>
</NonbondedForce>
</ForceField>