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Commit d1caf109 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1641 from jchodera/gb-cleanup 

Change variable 'q' to 'charge' in custom gb models
parents 38d967b2 d02f75ff
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Showing with 15 additions and 15 deletions
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ d1caf109
......@@ -353,13 +353,13 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
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"+params,
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-exp(-kappa*B)/solventDielectric)*charge^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"+params,
force.addEnergyTerm("-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*charge^2/B"+params,
CustomGBForce.SingleParticle)
if SA=='ACE':
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
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;"
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)
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)
else:
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)
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)
......@@ -476,7 +476,7 @@ class CustomAmberGBForceBase(CustomGBForce):
class GBSAHCTForce(CustomAmberGBForceBase):
"""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
----------
......@@ -499,7 +499,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
cutoff=None, kappa=0.0):
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -537,7 +537,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
class GBSAOBC1Force(CustomAmberGBForceBase):
"""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
----------
......@@ -561,7 +561,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -599,7 +599,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
class GBSAOBC2Force(GBSAOBC1Force):
"""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
----------
......@@ -625,7 +625,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
# is different. We inherit for getStandardParameters.
CustomAmberGBForceBase.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # 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);"
......@@ -641,7 +641,7 @@ class GBSAOBC2Force(GBSAOBC1Force):
class GBSAGBnForce(CustomAmberGBForceBase):
"""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
----------
......@@ -746,7 +746,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
CustomGBForce.addParticle(self, p + [radIndex])
def _addEnergyTerms(self):
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("radindex")
......@@ -834,7 +834,7 @@ class GBSAGBn2Force(GBSAGBnForce):
return radii
def _addEnergyTerms(self):
self.addPerParticleParameter("q")
self.addPerParticleParameter("charge")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha")
......
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