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Commit 85020137 authored by peastman's avatar peastman
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Merge pull request #275 from swails/master 

Fixes salt concentration for GB with a cutoff
parents 291484f2 2cbb8f43
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Showing with 12 additions and 4 deletions
wrappers/python/simtk/openmm/app/internal/customgbforces.py
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...@@ -206,11 +206,19 @@ def _createEnergyTerms(force, SA, cutoff, kappa): ...@@ -206,11 +206,19 @@ def _createEnergyTerms(force, SA, cutoff, kappa):
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:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2/f;" if kappa > 0:
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions) 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)
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)
else: else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");" if kappa > 0:
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce.ParticlePairNoExclusions) 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)
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)
""" """
Amber Equivalent: igb = 1 Amber Equivalent: igb = 1
......
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