def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0): """ 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("or") # Offset radius custom.addPerParticleParameter("sr") # Scaled offset radius custom.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2)) custom.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2)) custom.addComputedValue("I", "Ivdw+neckScale*Ineck;" "Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);" "Ivdw=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;" "L=max(or1, D);" "D=abs(r-sr2);" "radius1=or1+offset; radius2=or2+offset;" "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);" "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009) return custom
def GBSAGBnForce(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0): """ 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("or") # Offset radius custom.addPerParticleParameter("sr") # Scaled offset radius custom.addTabulatedFunction("getd0", Discrete1DFunction(d0)) custom.addTabulatedFunction("getm0", Discrete1DFunction(m0)) 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)*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;" "L=max(or1, D);" "D=abs(r-sr2);" "radius1=or1+offset; radius2=or2+offset;" "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);" "psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009) return custom
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0): """ 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") 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("getm0", Discrete1DFunction(m0)) 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)*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;" "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, kappa) return custom
def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None, cutoff=None, kappa=0.0): """ 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("or") # Offset radius custom.addPerParticleParameter("sr") # Scaled offset radius custom.addPerParticleParameter("alpha") custom.addPerParticleParameter("beta") custom.addPerParticleParameter("gamma") custom.addTabulatedFunction( "getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2)) custom.addTabulatedFunction( "getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2)) custom.addComputedValue( "I", "Ivdw+neckScale*Ineck;" "Ineck=step(radius1+radius2+neckCut-r)*getm0(radius1,radius2)/(1+100*(r-getd0(radius1,radius2))^2+0.3*1000000*(r-getd0(radius1,radius2))^6);" "Ivdw=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;" "L=max(or1, D);" "D=abs(r-sr2);" "radius1=or1+offset; radius2=or2+offset;" "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);" "psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle) _createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141) return custom