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Commit 98652498 authored by peastman's avatar peastman
Browse files

Merge pull request #667 from peastman/gb 

Optimizations to the custom GB models
parents 55bae85f 5bed3590
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Showing with 470 additions and 92 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 98652498
......@@ -43,7 +43,7 @@ import simtk.unit as u
from simtk.openmm.app import (forcefield as ff, Topology, element)
from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force)
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force, convertParameters)
# CHARMM imports
from simtk.openmm.app.internal.charmm.topologyobjects import (
ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral,
......@@ -1374,6 +1374,7 @@ class CharmmPsfFile(object):
if implicitSolvent is not None:
if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent)
gb_parms = convertParameters(gb_parms, str(implicitSolvent))
# If implicitSolventKappa is None, compute it from salt
# concentration
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 98652498
......@@ -1032,6 +1032,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers)
gb_parms = prmtop.getGBParms(gbmodel, elements)
if gbmodel != 'OBC2' or implicitSolventKappa != 0:
gb_parms = customgb.convertParameters(gb_parms, gbmodel)
if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
elif gbmodel == 'OBC1':
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 98652498
......@@ -189,36 +189,39 @@ for i in range (len(d0)):
m0[i]=m0[i]*10
def _createEnergyTerms(force, SA, cutoff, kappa):
def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, kappa, offset):
# Add the energy terms to the CustomGBForce. These are identical for all the GB models.
params = "; solventDielectric=%.16g; soluteDielectric=%.16g; kappa=%.16g; offset=%.16g" % (solventDielectric, soluteDielectric, kappa, offset)
if cutoff is not None:
params += "; cutoff=%.16g" % cutoff
if kappa > 0:
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*q^2/B",
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*q^2/B"+params,
CustomGBForce.SingleParticle)
elif kappa < 0:
# Do kappa check here to avoid repeating code everywhere
raise ValueError('kappa/ionic strength must be >= 0')
else:
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B",
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B"+params,
CustomGBForce.SingleParticle)
if SA=='ACE':
force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6", CustomGBForce.SingleParticle)
force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6; radius=or+offset"+params, CustomGBForce.SingleParticle)
elif SA is not None:
raise ValueError('Unknown surface area method: '+SA)
if cutoff is None:
if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else:
if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-kappa/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions)
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
"""
Amber Equivalent: igb = 1
......@@ -231,22 +234,15 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-I);"
"or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
custom.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
"""
......@@ -258,22 +254,16 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
"""
......@@ -285,22 +275,16 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
"""
......@@ -321,15 +305,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addGlobalParameter("neckScale", 0.361825)
custom.addGlobalParameter("neckCut", 0.68)
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
......@@ -341,12 +318,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
"radius1=or1+offset; radius2=or2+offset;"
"neckScale=0.361825; neckCut=0.68; offset=0.009", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(1.09511284*psi-1.907992938*psi^2+2.50798245*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
"""
......@@ -367,19 +344,12 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.0195141)
custom.addGlobalParameter("neckScale", 0.826836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
......@@ -390,10 +360,24 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
"radius1=or1+offset; radius2=or2+offset;"
"neckScale=0.826836; neckCut=0.68; offset=0.0195141", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa)
"psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
return custom
def convertParameters(params, gbmodel):
"""Convert the GB parameters from the file into the values expected by the appropriate CustomGBForce."""
newparams = [None]*len(params)
if gbmodel == 'GBn2':
offset = 0.0195141
else:
offset = 0.009
for i in range(len(params)):
newparams[i] = list(params[i])
newparams[i][0] -= offset
newparams[i][1] *= newparams[i][0]
return newparams
\ No newline at end of file
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ 98652498
......@@ -100,24 +100,13 @@ class TestAmberPrmtopFile(unittest.TestCase):
for method in methodMap:
system = prmtop2.createSystem(implicitSolvent=implicitSolvent_value,
solventDielectric=50.0, soluteDielectric=0.9, nonbondedMethod=method)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
if implicitSolvent_value in set([HCT, OBC1, GBn]):
for force in system.getForces():
if isinstance(force, CustomGBForce):
self.assertEqual(force.getNonbondedMethod(), methodMap[method])
for j in range(force.getNumGlobalParameters()):
if (force.getGlobalParameterName(j) == 'solventDielectric' and
force.getGlobalParameterDefaultValue(j) == 50.0):
found_matching_solvent_dielectric = True
if (force.getGlobalParameterName(j) == 'soluteDielectric' and
force.getGlobalParameterDefaultValue(j) == 0.9):
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertEqual(force.getNonbondedMethod(), methodMap[method])
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
else:
for force in system.getForces():
if isinstance(force, GBSAOBCForce):
......@@ -240,6 +229,25 @@ class TestAmberPrmtopFile(unittest.TestCase):
# Make sure the energy is relatively close to the value we get with
# Amber using this force field.
self.assertAlmostEqual(-7307.2735621/ene, 1, places=3)
def test_ImplicitSolventForces(self):
"""Compute forces for different implicit solvent types, and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
solventType = [HCT, OBC1, OBC2, GBn, GBn2]
nonbondedMethod = [NoCutoff, CutoffNonPeriodic, CutoffNonPeriodic, NoCutoff, NoCutoff]
salt = [0.0, 0.0, 0.5, 0.5, 0.0]*(moles/liter)
file = ['HCT_NoCutoff', 'OBC1_NonPeriodic', 'OBC2_NonPeriodic_Salt', 'GBn_NoCutoff_Salt', 'GBn2_NoCutoff']
pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
for i in range(5):
system = prmtop2.createSystem(implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName("CPU"))
context.setPositions(pdb.positions)
state1 = context.getState(getForces=True)
state2 = XmlSerializer.deserialize(open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml').read())
for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestCharmmFiles.py
View file @ 98652498
......@@ -69,21 +69,9 @@ class TestCharmmFiles(unittest.TestCase):
system = self.psf_x.createSystem(self.params, implicitSolvent=GBn,
solventDielectric=50.0,
soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
for force in system.getForces():
if isinstance(force, CustomGBForce):
for i in range(force.getNumGlobalParameters()):
if force.getGlobalParameterName(i) == 'solventDielectric':
if force.getGlobalParameterDefaultValue(i) == 50.0:
found_matching_solvent_dielectric = True
elif force.getGlobalParameterName(i) == 'soluteDielectric':
if force.getGlobalParameterDefaultValue(i) == 0.9:
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
def test_HydrogenMass(self):
"""Test that altering the mass of hydrogens works correctly."""
......@@ -127,6 +115,26 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_ImplicitSolventForces(self):
"""Compute forces for different implicit solvent types, and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
solventType = [HCT, OBC1, OBC2, GBn, GBn2]
nonbondedMethod = [NoCutoff, CutoffNonPeriodic, CutoffNonPeriodic, NoCutoff, NoCutoff]
salt = [0.0, 0.0, 0.5, 0.5, 0.0]*(moles/liter)
file = ['HCT_NoCutoff', 'OBC1_NonPeriodic', 'OBC2_NonPeriodic_Salt', 'GBn_NoCutoff_Salt', 'GBn2_NoCutoff']
for i in range(5):
system = self.psf_c.createSystem(self.params, implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName("CPU"))
context.setPositions(self.pdb.positions)
state1 = context.getState(getForces=True)
#out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
#out.write(XmlSerializer.serialize(state1))
#out.close()
state2 = XmlSerializer.deserialize(open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml').read())
for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/ala-ala-ala-implicit-forces/GBn2_NoCutoff.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
<PeriodicBoxVectors>
<A x="2" y="0" z="0"/>
<B x="0" y="2" z="0"/>
<C x="0" y="0" z="2"/>
</PeriodicBoxVectors>
<Forces>
<Force x="183.12361104909448" y="155.26784211796442" z="34.691159962151325"/>
<Force x="58.02808994091839" y="161.1479771333285" z="-6.905719184803445"/>
<Force x="53.116947200286404" y="-197.39924721297302" z="-191.13127107770634"/>
<Force x="46.218727097648014" y="-212.66428112142592" z="171.32495750170045"/>
<Force x="-143.51220792224802" y="-77.6749878542526" z="106.54286260678916"/>
<Force x="-122.2580981087889" y="-56.69313081273846" z="155.02475224419112"/>
<Force x="256.861210924291" y="4.991885101995734" z="56.89967589615151"/>
<Force x="-50.134423267799164" y="26.69582029770774" z="-148.0309316306637"/>
<Force x="93.82349928954996" y="-98.75344995978912" z="-30.84769608742689"/>
<Force x="-41.91077517758289" y="59.289304779748626" z="-110.90263298668452"/>
<Force x="-402.5528947784169" y="-502.5128785408756" z="146.8525667854756"/>
<Force x="140.35927800593402" y="706.2615945572692" z="-116.71709633774552"/>
<Force x="336.6168876754595" y="357.247339062576" z="-34.749492380483105"/>
<Force x="-415.7108187560625" y="-212.13687180023163" z="100.590812009496"/>
<Force x="-2064.878698363039" y="-1169.1702011127431" z="-141.28708209576615"/>
<Force x="-194.9400953435316" y="-24.670932939610708" z="11.635635952592624"/>
<Force x="-733.9608254321217" y="-237.08948410189265" z="-552.6426811401486"/>
<Force x="-1060.8507100087338" y="-17.22971806538561" z="-834.9535646446606"/>
<Force x="-11.966996404264762" y="-67.77194077117352" z="-66.3175636555273"/>
<Force x="-5.938422468557391" y="-.8846999866901797" z="-79.25483041064173"/>
<Force x="-535049.450575994" y="-759418.9456168906" z="-62586.54371173267"/>
<Force x="-811.1877273151022" y="-752.1488295390167" z="-559.2811902937815"/>
<Force x="-59122.721636109374" y="-11224.366289486006" z="4161.654215282473"/>
<Force x="8491.852921433589" y="-4987.486057146457" z="198.97782166846662"/>
<Force x="-92073.12391443842" y="-81863.60475973453" z="-3121.980801468735"/>
<Force x="629672.3177092219" y="832975.8356195987" z="70299.92572789358"/>
<Force x="137697.00593367853" y="-29842.060582353926" z="13288.173983467228"/>
<Force x="-16855.75815442956" y="-20321.644238398876" z="-2810.1468347196355"/>
<Force x="-35343.17474223994" y="19898.531265412435" z="9385.986414694597"/>
<Force x="-6566690.1522480175" y="1625423.158741199" z="-3339704.996853593"/>
<Force x="8959691.989050966" y="469395.856032878" z="202260.29458456024"/>
<Force x="-1344238.7618171684" y="1727648.777500562" z="3128189.6150764455"/>
<Force x="-1081288.5392807235" y="-3765528.083662639" z="-17472.013005055705"/>
</Forces>
</State>
wrappers/python/tests/systems/ala-ala-ala-implicit-forces/GBn_NoCutoff_Salt.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
<PeriodicBoxVectors>
<A x="2" y="0" z="0"/>
<B x="0" y="2" z="0"/>
<C x="0" y="0" z="2"/>
</PeriodicBoxVectors>
<Forces>
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/HCT_NoCutoff.xml 0 → 100644
View file @ 98652498
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC1_NonPeriodic.xml 0 → 100644
View file @ 98652498
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC2_NonPeriodic_Salt.xml 0 → 100644
View file @ 98652498
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/GBn2_NoCutoff.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/GBn_NoCutoff_Salt.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/HCT_NoCutoff.xml 0 → 100644
View file @ 98652498
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/OBC1_NonPeriodic.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/OBC2_NonPeriodic_Salt.xml 0 → 100644
View file @ 98652498
<?xml version="1.0" ?>
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