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Commit d02f75ff authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
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Change variable 'q' to 'charge' in custom gb models

parent e5be7821
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Showing with 15 additions and 15 deletions
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ d02f75ff
...@@ -353,13 +353,13 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -353,13 +353,13 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
if cutoff is not None: if cutoff is not None:
params += "; cutoff=%.16g" % cutoff 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"+params, force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*charge^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"+params, force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*charge^2/B"+params,
CustomGBForce.SingleParticle) CustomGBForce.SingleParticle)
if SA=='ACE': if SA=='ACE':
force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6; radius=or+offset"+params, CustomGBForce.SingleParticle) force.addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6; radius=or+offset"+params, CustomGBForce.SingleParticle)
...@@ -367,17 +367,17 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -367,17 +367,17 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
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)*charge1*charge2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, 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)*charge1*charge2/f;"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, 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-exp(-kappa*f)/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*charge1*charge2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, 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)*charge1*charge2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
...@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce): ...@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce):
class GBSAHCTForce(CustomAmberGBForceBase): class GBSAHCTForce(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=1`` """This class is equivalent to Amber ``igb=1``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase): ...@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
cutoff=None, kappa=0.0): cutoff=None, kappa=0.0):
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.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);" self.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);"
...@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase): ...@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
class GBSAOBC1Force(CustomAmberGBForceBase): class GBSAOBC1Force(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=2`` """This class is equivalent to Amber ``igb=2``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase): ...@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.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);" self.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);"
...@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase): ...@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
class GBSAOBC2Force(GBSAOBC1Force): class GBSAOBC2Force(GBSAOBC1Force):
"""This class is equivalent to Amber ``igb=5`` """This class is equivalent to Amber ``igb=5``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force): ...@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
# is different. We inherit for getStandardParameters. # is different. We inherit for getStandardParameters.
CustomAmberGBForceBase.__init__(self) CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.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);" self.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);"
...@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force): ...@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
class GBSAGBnForce(CustomAmberGBForceBase): class GBSAGBnForce(CustomAmberGBForceBase):
"""This class is equivalent to Amber ``igb=7`` """This class is equivalent to Amber ``igb=7``
The list of parameters to ``addParticle`` is: ``[q, or, sr]``. The list of parameters to ``addParticle`` is: ``[charge, or, sr]``.
Parameters Parameters
---------- ----------
...@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase): ...@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
CustomGBForce.addParticle(self, p + [radIndex]) CustomGBForce.addParticle(self, p + [radIndex])
def _addEnergyTerms(self): def _addEnergyTerms(self):
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("radindex") self.addPerParticleParameter("radindex")
...@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce):
return radii return radii
def _addEnergyTerms(self): def _addEnergyTerms(self):
self.addPerParticleParameter("q") self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha") self.addPerParticleParameter("alpha")
......
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