Skip to content

GitLab

"wrappers/vscode:/vscode.git/clone" did not exist on "74ef3feed43483e06417e0837bb7af1ad9d99fc0"
Commit 50c7b54c authored by Jason Swails's avatar Jason Swails
Browse files

Convert CustomGBForce implementations of Amber models to subclasses.

parent c3a74403
Hide whitespace changes
Inline Side-by-side
Showing with 136 additions and 112 deletions
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 50c7b54c
......@@ -33,6 +33,12 @@ from __future__ import division
from __future__ import absolute_import
from simtk.openmm import CustomGBForce, Continuous2DFunction
import simtk.unit as u
def strip_unit(value, unit):
if not u.is_quantity(value):
return value
return value.value_in_unit(unit)
d0=[2.26685,2.32548,2.38397,2.44235,2.50057,2.55867,2.61663,2.67444,
2.73212,2.78965,2.84705,2.9043,2.96141,3.0184,3.07524,3.13196,
......@@ -227,146 +233,164 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
"""
Amber Equivalent: igb = 1
"""
class GBSAHCTForce(CustomGBForce):
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
custom = CustomGBForce()
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
CustomGBForce.__init__(self)
self.addPerParticleParameter("q")
self.add
self.addPerParticleParameter("q")
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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)",
CustomGBForce.ParticlePairNoExclusions)
self.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
"""
Amber Equivalents: igb = 2
"""
def GBSAOBC1Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
class GBSAOBC1Force(CustomGBForce):
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
custom = CustomGBForce()
CustomGBForce.__init__(self)
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
self.addPerParticleParameter("q")
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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*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
self.addComputedValue("B", "1/(1/or-tanh(0.8*psi+2.909125*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
"""
Amber Equivalents: igb = 5
"""
def GBSAOBC2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
class GBSAOBC2Force(CustomGBForce):
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
custom = CustomGBForce()
CustomGBForce.__init__(self)
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
custom.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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
self.addPerParticleParameter("q")
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);"
"U=r+sr2;"
"L=max(or1, D);"
"D=abs(r-sr2)", CustomGBForce.ParticlePairNoExclusions)
custom.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*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
self.addComputedValue("B", "1/(1/or-tanh(psi-0.8*psi^2+4.85*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
"""
Amber Equivalents: igb = 7
"""
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
"""
class GBSAGBnForce(CustomGBForce):
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)
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
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
CustomGBForce.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
self.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
self.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)
self.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(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
def addParticle(self, parameters):
parameters = list(parameters)
parameters[0] = strip_unit(parameters[0], u.elementary_charge)
parameters[1] = strip_unit(parameters[0], u.nanometer)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
CustomGBForce.addParticle(self, parameters)
def setParticleParameters(self, idx, parameters):
parameters = list(parameters)
parameters[0] = strip_unit(parameters[0], u.elementary_charge)
parameters[1] = strip_unit(parameters[0], u.nanometer)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
CustomGBForce.setParticleParameters(self, idx, parameters)
"""
Amber Equivalents: igb = 8
"""
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
"""
class GBSAGBn2Force(CustomGBForce):
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
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
CustomGBForce.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
self.addPerParticleParameter("alpha")
self.addPerParticleParameter("beta")
self.addPerParticleParameter("gamma")
self.addTabulatedFunction("getd0", Continuous2DFunction(21, 21, d0, 0.1, 0.2, 0.1, 0.2))
self.addTabulatedFunction("getm0", Continuous2DFunction(21, 21, m0, 0.1, 0.2, 0.1, 0.2))
self.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)
self.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(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
def addParticle(self, parameters):
parameters = list(parameters)
parameters[0] = strip_unit(parameters[0], u.elementary_charge)
parameters[1] = strip_unit(parameters[0], u.nanometer)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
CustomGBForce.addParticle(self, parameters)
def setParticleParameters(self, idx, parameters):
parameters = list(parameters)
parameters[0] = strip_unit(parameters[0], u.elementary_charge)
parameters[1] = strip_unit(parameters[0], u.nanometer)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
CustomGBForce.setParticleParameters(self, idx, parameters)
def convertParameters(params, gbmodel):
"""Convert the GB parameters from the file into the values expected by the appropriate CustomGBForce."""
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment