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Commit b593e034 authored by Peter Eastman's avatar Peter Eastman
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Replaced TIP4P with TIP4P-Ew

parent e2d8c16e
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Showing with 32 additions and 2 deletions
wrappers/python/simtk/openmm/app/Modeller.py
View file @ b593e034
...@@ -105,7 +105,7 @@ class Modeller(object): ...@@ -105,7 +105,7 @@ class Modeller(object):
if sites == 4: if sites == 4:
newTopology.addAtom('M', None, newResidue) newTopology.addAtom('M', None, newResidue)
newPositions.append(0.74397587*po + 0.128012065*ph1 + 0.128012065*ph2) newPositions.append(0.786646558*po + 0.106676721*ph1 + 0.106676721*ph2)
elif sites == 5: elif sites == 5:
newTopology.addAtom('M1', None, newResidue) newTopology.addAtom('M1', None, newResidue)
newTopology.addAtom('M2', None, newResidue) newTopology.addAtom('M2', None, newResidue)
......
wrappers/python/simtk/openmm/app/data/tip4p.xml → wrappers/python/simtk/openmm/app/data/tip4pew.xml
View file @ b593e034
<ForceField> <ForceField>
<AtomTypes> <AtomTypes>
<Type name="tip4p-O" class="OW" element="O" mass="15.99943"/> <Type name="tip4pew-O" class="OW" element="O" mass="15.99943"/>
<Type name="tip4p-H" class="HW" element="H" mass="1.007947"/> <Type name="tip4pew-H" class="HW" element="H" mass="1.007947"/>
<Type name="tip4p-M" class="MW" mass="0"/> <Type name="tip4pew-M" class="MW" mass="0"/>
</AtomTypes> </AtomTypes>
<Residues> <Residues>
<Residue name="HOH"> <Residue name="HOH">
<Atom name="O" type="tip4p-O"/> <Atom name="O" type="tip4pew-O"/>
<Atom name="H1" type="tip4p-H"/> <Atom name="H1" type="tip4pew-H"/>
<Atom name="H2" type="tip4p-H"/> <Atom name="H2" type="tip4pew-H"/>
<Atom name="M" type="tip4p-M"/> <Atom name="M" type="tip4pew-M"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.74397587" weight2="0.128012065" weight3="0.128012065"/> <VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond from="0" to="1"/> <Bond from="0" to="1"/>
<Bond from="0" to="2"/> <Bond from="0" to="2"/>
</Residue> </Residue>
...@@ -22,9 +22,9 @@ ...@@ -22,9 +22,9 @@
<Angle class1="HW" class2="OW" class3="HW" angle="1.82421813418" k="836.8"/> <Angle class1="HW" class2="OW" class3="HW" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce> </HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5"> <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="tip4p-O" charge="0" sigma="0.315365" epsilon="0.64852"/> <Atom type="tip4pew-O" charge="0" sigma="0.315365" epsilon="0.64852"/>
<Atom type="tip4p-H" charge="0.52" sigma="1" epsilon="0"/> <Atom type="tip4pew-H" charge="0.52422" sigma="1" epsilon="0"/>
<Atom type="tip4p-M" charge="-1.04" sigma="1" epsilon="0"/> <Atom type="tip4pew-M" charge="-1.04844" sigma="1" epsilon="0"/>
</NonbondedForce> </NonbondedForce>
</ForceField> </ForceField>
wrappers/python/simtk/openmm/app/modeller.py
View file @ b593e034
...@@ -105,7 +105,7 @@ class Modeller(object): ...@@ -105,7 +105,7 @@ class Modeller(object):
if sites == 4: if sites == 4:
newTopology.addAtom('M', None, newResidue) newTopology.addAtom('M', None, newResidue)
newPositions.append(0.74397587*po + 0.128012065*ph1 + 0.128012065*ph2) newPositions.append(0.786646558*po + 0.106676721*ph1 + 0.106676721*ph2)
elif sites == 5: elif sites == 5:
newTopology.addAtom('M1', None, newResidue) newTopology.addAtom('M1', None, newResidue)
newTopology.addAtom('M2', None, newResidue) newTopology.addAtom('M2', None, newResidue)
......
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