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Commit 98652498 authored by peastman's avatar peastman
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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 ...@@ -43,7 +43,7 @@ import simtk.unit as u
from simtk.openmm.app import (forcefield as ff, Topology, element) 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.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce, from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force) GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force, convertParameters)
# CHARMM imports # CHARMM imports
from simtk.openmm.app.internal.charmm.topologyobjects import ( from simtk.openmm.app.internal.charmm.topologyobjects import (
ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral, ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral,
...@@ -1374,6 +1374,7 @@ class CharmmPsfFile(object): ...@@ -1374,6 +1374,7 @@ class CharmmPsfFile(object):
if implicitSolvent is not None: if implicitSolvent is not None:
if verbose: print('Adding GB parameters...') if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent) gb_parms = self._get_gb_params(implicitSolvent)
gb_parms = convertParameters(gb_parms, str(implicitSolvent))
# If implicitSolventKappa is None, compute it from salt # If implicitSolventKappa is None, compute it from salt
# concentration # 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 ...@@ -1032,6 +1032,8 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
if units.is_quantity(cutoff): if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers) cutoff = cutoff.value_in_unit(units.nanometers)
gb_parms = prmtop.getGBParms(gbmodel, elements) gb_parms = prmtop.getGBParms(gbmodel, elements)
if gbmodel != 'OBC2' or implicitSolventKappa != 0:
gb_parms = customgb.convertParameters(gb_parms, gbmodel)
if gbmodel == 'HCT': if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa) gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
elif gbmodel == 'OBC1': elif gbmodel == 'OBC1':
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 98652498
...@@ -189,36 +189,39 @@ for i in range (len(d0)): ...@@ -189,36 +189,39 @@ for i in range (len(d0)):
m0[i]=m0[i]*10 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. # 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: 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) CustomGBForce.SingleParticle)
elif kappa < 0: elif kappa < 0:
# Do kappa check here to avoid repeating code everywhere # Do kappa check here to avoid repeating code everywhere
raise ValueError('kappa/ionic strength must be >= 0') raise ValueError('kappa/ionic strength must be >= 0')
else: 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) CustomGBForce.SingleParticle)
if SA=='ACE': 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: elif SA is not None:
raise ValueError('Unknown surface area method: '+SA) raise ValueError('Unknown surface area method: '+SA)
if cutoff is None: if cutoff is None:
if kappa > 0: if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2/f;" 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: else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;" 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: else:
if kappa > 0: if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-kappa/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" 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: else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" 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 Amber Equivalent: igb = 1
...@@ -231,22 +234,15 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -231,22 +234,15 @@ def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q") custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius") custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("scale") custom.addPerParticleParameter("sr") # Scaled offset radius
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
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);" 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;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-I);" custom.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
"or=radius-offset", CustomGBForce.SingleParticle) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
_createEnergyTerms(custom, SA, cutoff, kappa)
return custom return custom
""" """
...@@ -258,22 +254,16 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -258,22 +254,16 @@ def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q") custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius") custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("scale") custom.addPerParticleParameter("sr") # Scaled offset radius
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
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);" 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;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);" custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom return custom
""" """
...@@ -285,22 +275,16 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -285,22 +275,16 @@ def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q") custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius") custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("scale") custom.addPerParticleParameter("sr") # Scaled offset radius
if kappa > 0: custom.addGlobalParameter('kappa', kappa)
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
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);" 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;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);" 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) "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom return custom
""" """
...@@ -321,15 +305,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -321,15 +305,8 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q") custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius") custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("scale") custom.addPerParticleParameter("sr") # Scaled offset radius
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.addTabulatedFunction("getd0", Discrete1DFunction(d0)) custom.addTabulatedFunction("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0)) custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
...@@ -341,12 +318,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -341,12 +318,12 @@ def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2);"
"sr2 = scale2*or2;" "radius1=or1+offset; radius2=or2+offset;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions) "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);" 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) "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom return custom
""" """
...@@ -367,19 +344,12 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -367,19 +344,12 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
custom = CustomGBForce() custom = CustomGBForce()
custom.addPerParticleParameter("q") custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius") custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("scale") custom.addPerParticleParameter("sr") # Scaled offset radius
custom.addPerParticleParameter("alpha") custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta") custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma") 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("getd0", Discrete1DFunction(d0))
custom.addTabulatedFunction("getm0", Discrete1DFunction(m0)) custom.addTabulatedFunction("getm0", Discrete1DFunction(m0))
...@@ -390,10 +360,24 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, ...@@ -390,10 +360,24 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
"U=r+sr2;" "U=r+sr2;"
"L=max(or1, D);" "L=max(or1, D);"
"D=abs(r-sr2);" "D=abs(r-sr2);"
"sr2 = scale2*or2;" "radius1=or1+offset; radius2=or2+offset;"
"or1 = radius1-offset; or2 = radius2-offset", CustomGBForce.ParticlePairNoExclusions) "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);" custom.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; or=radius-offset", CustomGBForce.SingleParticle) "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, SA, cutoff, kappa) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
return custom 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): ...@@ -100,24 +100,13 @@ class TestAmberPrmtopFile(unittest.TestCase):
for method in methodMap: for method in methodMap:
system = prmtop2.createSystem(implicitSolvent=implicitSolvent_value, system = prmtop2.createSystem(implicitSolvent=implicitSolvent_value,
solventDielectric=50.0, soluteDielectric=0.9, nonbondedMethod=method) 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]): if implicitSolvent_value in set([HCT, OBC1, GBn]):
for force in system.getForces(): for force in system.getForces():
if isinstance(force, CustomGBForce): if isinstance(force, CustomGBForce):
self.assertEqual(force.getNonbondedMethod(), methodMap[method]) 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): if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0) self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertEqual(force.getNonbondedMethod(), methodMap[method]) self.assertEqual(force.getNonbondedMethod(), methodMap[method])
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
else: else:
for force in system.getForces(): for force in system.getForces():
if isinstance(force, GBSAOBCForce): if isinstance(force, GBSAOBCForce):
...@@ -241,5 +230,24 @@ class TestAmberPrmtopFile(unittest.TestCase): ...@@ -241,5 +230,24 @@ class TestAmberPrmtopFile(unittest.TestCase):
# Amber using this force field. # Amber using this force field.
self.assertAlmostEqual(-7307.2735621/ene, 1, places=3) 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__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/TestCharmmFiles.py
View file @ 98652498
...@@ -69,21 +69,9 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -69,21 +69,9 @@ class TestCharmmFiles(unittest.TestCase):
system = self.psf_x.createSystem(self.params, implicitSolvent=GBn, system = self.psf_x.createSystem(self.params, implicitSolvent=GBn,
solventDielectric=50.0, solventDielectric=50.0,
soluteDielectric = 0.9) soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
for force in system.getForces(): 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): if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0) self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
def test_HydrogenMass(self): def test_HydrogenMass(self):
"""Test that altering the mass of hydrogens works correctly.""" """Test that altering the mass of hydrogens works correctly."""
...@@ -127,6 +115,26 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -127,6 +115,26 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05) 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__': if __name__ == '__main__':
unittest.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"/>
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</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"/>
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/HCT_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"/>
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC1_NonPeriodic.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"/>
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC2_NonPeriodic_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"/>
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<Forces>
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wrappers/python/tests/systems/alanine-dipeptide-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"/>
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<Forces>
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/GBn_NoCutoff_Salt.xml 0 → 100644
View file @ 98652498
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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
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wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/OBC2_NonPeriodic_Salt.xml 0 → 100644
View file @ 98652498
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