def GBSAOBC1Force(solventDielectric=78.5,
soluteDielectric=1,
SA=None,
cutoff=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue(
"I",
"step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"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);"
"psi=I*or; or=radius-offset",
CustomGBForce.SingleParticle,
)
_createEnergyTerms(custom, SA, cutoff)
return custom
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.009)
custom.addComputedValue(
"I",
"step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"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);" "psi=I*or; or=radius-offset",
CustomGBForce.SingleParticle,
)
_createEnergyTerms(custom, SA, cutoff)
return custom
def GBSAGBn2Force(solventDielectric=78.5,
soluteDielectric=1,
SA=None,
cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.019_514_1)
custom.addGlobalParameter("neckScale", 0.826_836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue(
"I",
"Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset",
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)
return custom
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None):
"""
Indexing for tables:
input: radius1, radius2
index = (radius2*200-20)*21 + (radius1*200-20)
output: index of desired value in row-by-row, 1D version of Tables 3 & 4
"""
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("radius")
custom.addPerParticleParameter("scale")
custom.addPerParticleParameter("alpha")
custom.addPerParticleParameter("beta")
custom.addPerParticleParameter("gamma")
custom.addGlobalParameter("solventDielectric", solventDielectric)
custom.addGlobalParameter("soluteDielectric", soluteDielectric)
custom.addGlobalParameter("offset", 0.019_514_1)
custom.addGlobalParameter("neckScale", 0.826_836)
custom.addGlobalParameter("neckCut", 0.68)
custom.addFunction("getd0", d0, 0, 440)
custom.addFunction("getm0", m0, 0, 440)
custom.addComputedValue(
"I",
"Ivdw+neckScale*Ineck;"
"Ineck=step(radius1+radius2+neckCut-r)*getm0(index)/(1+100*(r-getd0(index))^2+0.3*1000000*(r-getd0(index))^6);"
"index = (radius2*200-20)*21 + (radius1*200-20);"
"Ivdw=step(r+sr2-or1)*excl*0.5*(1/L-1/U+0.25*(r-sr2^2/r)*(1/(U^2)-1/(L^2))+0.5*log(L/U)/r);"
"excl=step(abs(q1)-0.00000001)*step(abs(q2)-0.00000001);" # exclude pair where one atom is not charged
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2);"
"sr2 = scale2*or2;"
"or1 = radius1-offset; or2 = radius2-offset",
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)
return custom
