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Commit 90886d43 authored by peastman's avatar peastman
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Merge pull request #1310 from swails/gbfrc 

Change functions in `customgbforces.py` to subclasses
parents c3a74403 fc22bf19
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Showing with 130 additions and 120 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 90886d43
......@@ -47,7 +47,7 @@ import simtk.unit as u
from simtk.openmm.app import (forcefield as ff, Topology, element)
from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force, convertParameters)
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force)
from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
# CHARMM imports
from simtk.openmm.app.internal.charmm.topologyobjects import (
......@@ -1250,7 +1250,6 @@ class CharmmPsfFile(object):
if implicitSolvent is not None:
if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent)
gb_parms = convertParameters(gb_parms, str(implicitSolvent))
# If implicitSolventKappa is None, compute it from salt
# concentration
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 90886d43
......@@ -1054,8 +1054,6 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers)
gb_parms = prmtop.getGBParms(gbmodel, elements)
if gbmodel != 'OBC2' or implicitSolventKappa != 0:
gb_parms = customgb.convertParameters(gb_parms, gbmodel)
if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
elif gbmodel == 'OBC1':
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 90886d43
......@@ -32,7 +32,14 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
from __future__ import division
from __future__ import absolute_import
import copy
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,
......@@ -224,159 +231,165 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
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)))"+params, CustomGBForce.ParticlePairNoExclusions)
class CustomAmberGBForce(CustomGBForce):
OFFSET = 0.009
RADIUS_ARG_POSITION = 1
SCREEN_POSITION = 2
def __init__(self, *args, **kwargs):
raise NotImplementedError('Cannot instantiate ABC')
def addParticle(self, params):
params = copy.deepcopy(params)
params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
CustomGBForce.addParticle(self, params)
return params
def setParticleParameters(self, idx, params):
params = copy.deepcopy(params)
params[self.RADIUS_ARG_POSITION] = strip_unit(params[self.RADIUS_ARG_POSITION], u.nanometer) - self.OFFSET
params[self.SCREEN_POSITION] *= params[self.RADIUS_ARG_POSITION]
CustomGBForce.addParticle(self, params)
return params
"""
Amber Equivalent: igb = 1
"""
class GBSAHCTForce(CustomAmberGBForce):
def GBSAHCTForce(solventDielectric=78.5, soluteDielectric=1, SA=None,
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
CustomGBForce.__init__(self)
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)
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-I)", CustomGBForce.SingleParticle)
_createEnergyTerms(custom, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
return custom
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(CustomAmberGBForce):
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(CustomAmberGBForce):
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):
class GBSAGBnForce(CustomAmberGBForce):
def __init__(self, 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
"""
CustomGBForce.__init__(self)
self.addPerParticleParameter("q")
self.addPerParticleParameter("or") # Offset radius
self.addPerParticleParameter("sr") # Scaled offset radius
custom = CustomGBForce()
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))
custom.addPerParticleParameter("q")
custom.addPerParticleParameter("or") # Offset radius
custom.addPerParticleParameter("sr") # Scaled offset radius
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)
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))
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)
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 addParticle(self, parameters):
parameters = CustomAmberGBForce.addParticle(self, parameters)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
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 setParticleParameters(self, idx, parameters):
parameters = CustomAmberGBForce.setParticleParameters(self, idx, parameters)
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
"""
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
"""
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")
class GBSAGBn2Force(GBSAGBnForce):
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))
OFFSET = 0.0195141
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
def convertParameters(params, gbmodel):
"""Convert the GB parameters from the file into the values expected by the appropriate CustomGBForce."""
if gbmodel == 'GBn2':
offset = 0.0195141
else:
offset = 0.009
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
for p in params:
newParam = list(p)
newParam[0] -= offset
newParam[1] *= newParam[0]
yield newParam
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)
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