def grosberg_angle(sim_object, triplets, k=1.5, name="grosberg_angle"):
"""Adds stiffness according to the Grosberg paper.
(Halverson, Jonathan D., et al. "Molecular dynamics simulation study of
nonconcatenated ring polymers in a melt. I. Statics."
The Journal of chemical physics 134 (2011): 204904.)
Parameters are synchronized with normal stiffness
If k is an array, it has to be of the length N.
Xth value then specifies stiffness of the angle centered at
monomer number X.
Values for ends of the chain will be simply ignored.
Parameters
----------
k : float or N-long list of floats
Synchronized with regular stiffness.
Default value is very flexible, as in Grosberg paper.
Default value maximizes entanglement length.
"""
k = _to_array_1d(k, len(triplets))
force = openmm.CustomAngleForce("GRk * kT * (1 - cos(theta - 3.141592))")
force.name = name
force.addGlobalParameter("kT", sim_object.kT)
force.addPerAngleParameter("GRk")
for triplet_idx, (p1, p2, p3) in enumerate(triplets):
force.addAngle(p1, p2, p3, [k[triplet_idx]])
return force
def angle_force(sim_object,
triplets,
k=1.5,
theta_0=np.pi,
name="angle",
override_checks=False):
"""Adds harmonic angle bonds. k specifies energy in kT at one radian
If k is an array, it has to be of the length N.
Xth value then specifies stiffness of the angle centered at
monomer number X.
Values for ends of the chain will be simply ignored.
Parameters
----------
k : float or list of length N
Stiffness of the bond.
If list, then determines the stiffness of the i-th triplet
Potential is k * alpha^2 * 0.5 * kT
theta_0 : float or list of length N
Equilibrium angle of the bond. By default it is np.pi.
override_checks: bool
If True then do not check that no bonds are repeated.
False by default.
"""
# check for repeated triplets
if not override_checks:
_check_angle_bonds(triplets)
k = _to_array_1d(k, len(triplets))
theta_0 = _to_array_1d(theta_0, len(triplets))
energy = "kT*angK * (theta - angT0) * (theta - angT0) * (0.5)"
force = openmm.CustomAngleForce(energy)
force.name = name
force.addGlobalParameter("kT", sim_object.kT)
force.addPerAngleParameter("angK")
force.addPerAngleParameter("angT0")
for triplet_idx, (p1, p2, p3) in enumerate(triplets):
force.addAngle(int(p1), int(p2), int(p3),
(float(k[triplet_idx]), float(theta_0[triplet_idx])))
return force
def _get_internal_from_omm(atom_coords, bond_coords, angle_coords, torsion_coords):
import copy
#master system, will be used for all three
sys = openmm.System()
platform = openmm.Platform.getPlatformByName("Reference")
for i in range(4):
sys.addParticle(1.0*unit.amu)
#first, the bond length:
bond_sys = openmm.System()
bond_sys.addParticle(1.0*unit.amu)
bond_sys.addParticle(1.0*unit.amu)
bond_force = openmm.CustomBondForce("r")
bond_force.addBond(0, 1, [])
bond_sys.addForce(bond_force)
bond_integrator = openmm.VerletIntegrator(1*unit.femtoseconds)
bond_context = openmm.Context(bond_sys, bond_integrator, platform)
bond_context.setPositions([atom_coords, bond_coords])
bond_state = bond_context.getState(getEnergy=True)
r = bond_state.getPotentialEnergy()
del bond_sys, bond_context, bond_integrator
#now, the angle:
angle_sys = copy.deepcopy(sys)
angle_force = openmm.CustomAngleForce("theta")
angle_force.addAngle(0,1,2,[])
angle_sys.addForce(angle_force)
angle_integrator = openmm.VerletIntegrator(1*unit.femtoseconds)
angle_context = openmm.Context(angle_sys, angle_integrator, platform)
angle_context.setPositions([atom_coords, bond_coords, angle_coords, torsion_coords])
angle_state = angle_context.getState(getEnergy=True)
theta = angle_state.getPotentialEnergy()
del angle_sys, angle_context, angle_integrator
#finally, the torsion:
torsion_sys = copy.deepcopy(sys)
torsion_force = openmm.CustomTorsionForce("theta")
torsion_force.addTorsion(0,1,2,3,[])
torsion_sys.addForce(torsion_force)
torsion_integrator = openmm.VerletIntegrator(1*unit.femtoseconds)
torsion_context = openmm.Context(torsion_sys, torsion_integrator, platform)
torsion_context.setPositions([atom_coords, bond_coords, angle_coords, torsion_coords])
torsion_state = torsion_context.getState(getEnergy=True)
phi = torsion_state.getPotentialEnergy()
del torsion_sys, torsion_context, torsion_integrator
return r, theta, phi
def _add_angle_force_terms(self):
core_energy_expression = '(K/2)*(theta-theta0)^2;'
core_energy_expression += 'K = k*scale_factor;' # linearly interpolate spring constant
core_energy_expression += self.scaling_expression()
# Create the force and add the relevant parameters
custom_core_force = openmm.CustomAngleForce(core_energy_expression)
custom_core_force.addPerAngleParameter('theta0')
custom_core_force.addPerAngleParameter('k')
custom_core_force.addPerAngleParameter('identifier')
custom_core_force.addGlobalParameter('solute_scale', 1.0)
custom_core_force.addGlobalParameter('inter_scale', 1.0)
self._out_system.addForce(custom_core_force)
self._out_system_forces[
custom_core_force.__class__.__name__] = custom_core_force
def modify_harmonic_angles(self):
"""
turn the harmonic angles into a custom angle force
lambda_protocol :
- 'lambda_MM_angles' : 1 -> 0
- 'lambda_scale' : beta / beta0
"""
self._alchemical_to_old_angles = {}
angle_expression = 'lambda_MM_angles * lambda_scale * (k/2)*(theta-theta0)^2;'
custom_angle_force = openmm.CustomAngleForce(angle_expression)
#add the global params
custom_angle_force.addGlobalParameter('lambda_MM_angles', 1.)
custom_angle_force.addGlobalParameter('lambda_scale', 1.)
#add the perangleparams
custom_angle_force.addPerAngleParameter('theta0')
custom_angle_force.addPerAngleParameter('k')
#now to iterate over the angles.
for idx in range(self._system_forces['HarmonicAngleForce'].getNumAngles()):
p1, p2, p3, theta0, k = self._system_forces['HarmonicAngleForce'].getAngleParameters(idx)
if self.is_in_alchemical_region({p1,p2,p3}):
#first thing to do is to zero the force from the `HarmonicAngleForce`
self._system_forces['HarmonicAngleForce'].setAngleParameters(idx, p1, p2, p3, theta0, k*0.0)
self._endstate_system_forces['HarmonicAngleForce'].setAngleParameters(idx, p1, p2, p3, theta0, k*0.0)
#then add it to the custom angle force
custom_angle_idx = custom_angle_force.addAngle(p1, p2, p3, [theta0, k])
#add to the alchemical bonds dict for bookkeeping
self._alchemical_to_old_angles[custom_angle_idx] = idx
#then add the custom bond force to the system
if self._system_forces['HarmonicAngleForce'].usesPeriodicBoundaryConditions():
custom_angle_force.setUsesPeriodicBoundaryConditions(True)
self._system.addForce(custom_angle_force)
def _add_extras(system, bonds, restricted_angles, torsions):
# add the extra bonds
if bonds:
f = [f for f in system.getForces() if isinstance(f, mm.HarmonicBondForce)][0]
for bond in bonds:
f.addBond(bond.i, bond.j, bond.length, bond.force_constant)
# add the extra restricted_angles
if restricted_angles:
# create the new force for restricted angles
f = mm.CustomAngleForce(
"0.5 * k_ra * (theta - theta0_ra)^2 / sin(theta * 3.1459 / 180)"
)
f.addPerAngleParameter("k_ra")
f.addPerAngleParameter("theta0_ra")
for angle in restricted_angles:
f.addAngle(
angle.i,
angle.j,
angle.k,
(angle.force_constant, angle.angle),
)
system.addForce(f)
# add the extra torsions
if torsions:
f = [f for f in system.getForces() if isinstance(f, mm.PeriodicTorsionForce)][0]
for tors in torsions:
f.addTorsion(
tors.i,
tors.j,
tors.k,
tors.l,
tors.multiplicity,
tors.phase,
tors.energy,
)
def _addAngleToSystem(self, syst, moleculeType, bondedTypes, atomBonds,
baseAtomIndex):
degToRad = math.pi / 180
for fields in moleculeType.angles:
atoms = [int(x) - 1 for x in fields[:3]]
types = tuple(bondedTypes[i] for i in atoms)
if len(fields) >= 6:
params = fields[4:]
elif types in self.angleTypes:
params = self.angleTypes[types][4:]
elif types[::-1] in self.angleTypes:
params = self.angleTypes[types[::-1]][4:]
else:
raise ValueError('No parameters specified for angle: ' +
fields[0] + ', ' + fields[1] + ', ' +
fields[2])
#angles = mm.HarmonicAngleForce()
theta = float(params[0]) * degToRad
if int(fields[3]) == 2:
gromosAngle = mm.CustomAngleForce(
'0.5*k*(cos(theta)-cos(theta0))^2')
gromosAngle.addPerAngleParameter('theta0')
gromosAngle.addPerAngleParameter('k')
syst.addForce(gromosAngle)
gromosAngle.addAngle(baseAtomIndex + atoms[0],
baseAtomIndex + atoms[1],
baseAtomIndex + atoms[2],
[theta, float(params[1])])
elif int(fields[3]) == 1:
angles = mm.HarmonicAngleForce()
angles.addAngle(baseAtomIndex + atoms[0],
baseAtomIndex + atoms[1],
baseAtomIndex + atoms[2], theta,
float(params[1]))
def angle_force(sim_object, triplets, k=1.5, theta_0=np.pi, name="angle"):
"""Adds harmonic angle bonds. k specifies energy in kT at one radian
If k is an array, it has to be of the length N.
Xth value then specifies stiffness of the angle centered at
monomer number X.
Values for ends of the chain will be simply ignored.
Parameters
----------
k : float or list of length N
Stiffness of the bond.
If list, then determines the stiffness of the i-th triplet
Potential is k * alpha^2 * 0.5 * kT
theta_0 : float or list of length N
Equilibrium angle of the bond. By default it is np.pi.
"""
k = _to_array_1d(k, len(triplets))
theta_0 = _to_array_1d(theta_0, len(triplets))
energy = "kT*angK * (theta - angT0) * (theta - angT0) * (0.5)"
force = openmm.CustomAngleForce(energy)
force.name = name
force.addGlobalParameter("kT", sim_object.kT)
force.addPerAngleParameter("angK")
force.addPerAngleParameter("angT0")
for triplet_idx, (p1, p2, p3) in enumerate(triplets):
force.addAngle(p1, p2, p3, [k[triplet_idx], theta_0[triplet_idx]])
return force
def add_molecule_to_system(system,
molecule_system,
core_atoms,
variant,
atoms_to_exclude=[]):
"""
Add the valence terms for the molecule from molecule_system.
Parameters
----------
system : simtk.openmm.System
The system object to which the valence terms are to be added.
molecule_system : simtk.openmm.System
The system object from which core valence terms are to be taken.
core_atoms : list of int
The list of atom indices within molecule_system corresponding to core atoms.
variant : int
The variant index of this molecule if not a core fragment, or 0 if this is a core fragment and only core atoms are to be added.
Returns
-------
mapping : dict of int
mapping[index] is the atom index in `system` corresponding to atom `index` within `molecule_system`.
"""
def _createCustomNonbondedForce(self,
system,
molecule_system,
softcore_alpha=0.5,
softcore_beta=12 * unit.angstrom**2):
"""
Create alchemically-modified version of NonbondedForce.
Parameters
----------
system : simtk.openmm.System
Alchemically-modified system being built. This object will be modified.
molecule_system : simtk.openmm.System
Source molecule system to copy from.
softcore_alpha : float, optional, default = 0.5
Alchemical softcore parameter for Lennard-Jones.
softcore_beta : simtk.unit.Quantity with units compatible with angstroms**2, optional, default = 12*angstrom**2
Alchemical softcore parameter for electrostatics.
TODO
----
Try using a single, common "reff" effective softcore distance for both Lennard-Jones and Coulomb.
"""
alchemical_atom_indices = self.ligand_atoms
# Create a copy of the NonbondedForce to handle non-alchemical interactions.
nonbonded_force = copy.deepcopy(reference_force)
system.addForce(nonbonded_force)
# Create CustomNonbondedForce objects to handle softcore interactions between alchemically-modified system and rest of system.
# Create atom groups.
natoms = system.getNumParticles()
atomset1 = set(
alchemical_atom_indices) # only alchemically-modified atoms
atomset2 = set(range(system.getNumParticles())
) # all atoms, including alchemical region
# CustomNonbondedForce energy expression.
sterics_energy_expression = ""
electrostatics_energy_expression = ""
# Select functional form based on nonbonded method.
method = reference_force.getNonbondedMethod()
if method in [openmm.NonbondedForce.NoCutoff]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = lambda_sterics*4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;"
# soft-core Coulomb
electrostatics_energy_expression += "U_electrostatics = ONE_4PI_EPS0*lambda_electrostatics*chargeprod/reff_electrostatics;"
elif method in [
openmm.NonbondedForce.CutoffPeriodic,
openmm.NonbondedForce.CutoffNonPeriodic
]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = lambda_sterics*4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;"
# reaction-field electrostatics
epsilon_solvent = reference_force.getReactionFieldDielectric()
r_cutoff = reference_force.getCutoffDistance()
electrostatics_energy_expression += "U_electrostatics = lambda_electrostatics*ONE_4PI_EPS0*chargeprod*(reff_electrostatics^(-1) + k_rf*reff_electrostatics^2 - c_rf);"
k_rf = r_cutoff**(-3) * ((epsilon_solvent - 1) /
(2 * epsilon_solvent + 1))
c_rf = r_cutoff**(-1) * ((3 * epsilon_solvent) /
(2 * epsilon_solvent + 1))
electrostatics_energy_expression += "k_rf = %f;" % (
k_rf / k_rf.in_unit_system(unit.md_unit_system).unit)
electrostatics_energy_expression += "c_rf = %f;" % (
c_rf / c_rf.in_unit_system(unit.md_unit_system).unit)
elif method in [
openmm.NonbondedForce.PME, openmm.NonbondedForce.Ewald
]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = lambda_sterics*4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;"
# Ewald direct-space electrostatics
[alpha_ewald, nx, ny, nz] = reference_force.getPMEParameters()
if alpha_ewald == 0.0:
# If alpha is 0.0, alpha_ewald is computed by OpenMM from from the error tolerance.
delta = reference_force.getEwaldErrorTolerance()
r_cutoff = reference_force.getCutoffDistance()
alpha_ewald = np.sqrt(-np.log(2 * delta)) / r_cutoff
electrostatics_energy_expression += "U_electrostatics = lambda_electrostatics*ONE_4PI_EPS0*chargeprod*erfc(alpha_ewald*reff_electrostatics)/reff_electrostatics;"
electrostatics_energy_expression += "alpha_ewald = %f;" % (
alpha_ewald /
alpha_ewald.in_unit_system(unit.md_unit_system).unit)
# TODO: Handle reciprocal-space electrostatics
else:
raise Exception("Nonbonded method %s not supported yet." %
str(method))
# Add additional definitions common to all methods.
sterics_energy_expression += "reff_sterics = sigma*((softcore_alpha*(1.-lambda_sterics) + (r/sigma)^6))^(1/6);" # effective softcore distance for sterics
sterics_energy_expression += "softcore_alpha = %f;" % softcore_alpha
electrostatics_energy_expression += "reff_electrostatics = sqrt(softcore_beta*(1.-lambda_electrostatics) + r^2);" # effective softcore distance for electrostatics
electrostatics_energy_expression += "softcore_beta = %f;" % (
softcore_beta /
softcore_beta.in_unit_system(unit.md_unit_system).unit)
electrostatics_energy_expression += "ONE_4PI_EPS0 = %f;" % ONE_4PI_EPS0 # already in OpenMM units
# Define mixing rules.
sterics_mixing_rules = ""
sterics_mixing_rules += "epsilon = sqrt(epsilon1*epsilon2);" # mixing rule for epsilon
sterics_mixing_rules += "sigma = 0.5*(sigma1 + sigma2);" # mixing rule for sigma
electrostatics_mixing_rules = ""
electrostatics_mixing_rules += "chargeprod = charge1*charge2;" # mixing rule for charges
# Create CustomNonbondedForce to handle interactions between alchemically-modified atoms and rest of system.
electrostatics_custom_nonbonded_force = openmm.CustomNonbondedForce(
"U_electrostatics;" + electrostatics_energy_expression +
electrostatics_mixing_rules)
electrostatics_custom_nonbonded_force.addGlobalParameter(
"lambda_electrostatics", 1.0)
electrostatics_custom_nonbonded_force.addPerParticleParameter(
"charge") # partial charge
sterics_custom_nonbonded_force = openmm.CustomNonbondedForce(
"U_sterics;" + sterics_energy_expression + sterics_mixing_rules)
sterics_custom_nonbonded_force.addGlobalParameter(
"lambda_sterics", 1.0)
sterics_custom_nonbonded_force.addPerParticleParameter(
"sigma") # Lennard-Jones sigma
sterics_custom_nonbonded_force.addPerParticleParameter(
"epsilon") # Lennard-Jones epsilon
# Set parameters to match reference force.
sterics_custom_nonbonded_force.setUseSwitchingFunction(
nonbonded_force.getUseSwitchingFunction())
electrostatics_custom_nonbonded_force.setUseSwitchingFunction(False)
sterics_custom_nonbonded_force.setCutoffDistance(
nonbonded_force.getCutoffDistance())
electrostatics_custom_nonbonded_force.setCutoffDistance(
nonbonded_force.getCutoffDistance())
sterics_custom_nonbonded_force.setSwitchingDistance(
nonbonded_force.getSwitchingDistance())
sterics_custom_nonbonded_force.setUseLongRangeCorrection(
nonbonded_force.getUseDispersionCorrection())
electrostatics_custom_nonbonded_force.setUseLongRangeCorrection(False)
# Set periodicity and cutoff parameters corresponding to reference Force.
if nonbonded_force.getNonbondedMethod() in [
openmm.NonbondedForce.Ewald, openmm.NonbondedForce.PME,
openmm.NonbondedForce.CutoffPeriodic
]:
sterics_custom_nonbonded_force.setNonbondedMethod(
openmm.CustomNonbondedForce.CutoffPeriodic)
electrostatics_custom_nonbonded_force.setNonbondedMethod(
openmm.CustomNonbondedForce.CutoffPeriodic)
else:
sterics_custom_nonbonded_force.setNonbondedMethod(
nonbonded_force.getNonbondedMethod())
electrostatics_custom_nonbonded_force.setNonbondedMethod(
nonbonded_force.getNonbondedMethod())
# Restrict interaction evaluation to be between alchemical atoms and rest of environment.
# TODO: Exclude intra-alchemical region if we are separately handling that through a separate CustomNonbondedForce for decoupling.
sterics_custom_nonbonded_force.addInteractionGroup(atomset1, atomset2)
electrostatics_custom_nonbonded_force.addInteractionGroup(
atomset1, atomset2)
# Add custom forces.
system.addForce(sterics_custom_nonbonded_force)
system.addForce(electrostatics_custom_nonbonded_force)
# Create CustomBondForce to handle exceptions for both kinds of interactions.
custom_bond_force = openmm.CustomBondForce(
"U_sterics + U_electrostatics;" + sterics_energy_expression +
electrostatics_energy_expression)
custom_bond_force.addGlobalParameter("lambda_electrostatics", 1.0)
custom_bond_force.addGlobalParameter("lambda_sterics", 1.0)
custom_bond_force.addPerBondParameter("chargeprod") # charge product
custom_bond_force.addPerBondParameter(
"sigma") # Lennard-Jones effective sigma
custom_bond_force.addPerBondParameter(
"epsilon") # Lennard-Jones effective epsilon
system.addForce(custom_bond_force)
# Move NonbondedForce particle terms for alchemically-modified particles to CustomNonbondedForce.
for particle_index in range(nonbonded_force.getNumParticles()):
# Retrieve parameters.
[charge, sigma,
epsilon] = nonbonded_force.getParticleParameters(particle_index)
# Add parameters to custom force handling interactions between alchemically-modified atoms and rest of system.
sterics_custom_nonbonded_force.addParticle([sigma, epsilon])
electrostatics_custom_nonbonded_force.addParticle([charge])
# Turn off Lennard-Jones contribution from alchemically-modified particles.
if particle_index in alchemical_atom_indices:
nonbonded_force.setParticleParameters(particle_index,
0 * charge, sigma,
0 * epsilon)
# Move NonbondedForce exception terms for alchemically-modified particles to CustomNonbondedForce/CustomBondForce.
for exception_index in range(nonbonded_force.getNumExceptions()):
# Retrieve parameters.
[iatom, jatom, chargeprod, sigma,
epsilon] = nonbonded_force.getExceptionParameters(exception_index)
# Exclude this atom pair in CustomNonbondedForce.
sterics_custom_nonbonded_force.addExclusion(iatom, jatom)
electrostatics_custom_nonbonded_force.addExclusion(iatom, jatom)
# Move exceptions involving alchemically-modified atoms to CustomBondForce.
if self.annihilate_sterics and (iatom in alchemical_atom_indices
) and (jatom
in alchemical_atom_indices):
# Add special CustomBondForce term to handle alchemically-modified Lennard-Jones exception.
custom_bond_force.addBond(iatom, jatom,
[chargeprod, sigma, epsilon])
# Zero terms in NonbondedForce.
nonbonded_force.setExceptionParameters(exception_index, iatom,
jatom, 0 * chargeprod,
sigma, 0 * epsilon)
# TODO: Add back NonbondedForce terms for alchemical system needed in case of decoupling electrostatics or sterics via second CustomBondForce.
# TODO: Also need to change current CustomBondForce to not alchemically disappear system.
return
# Build dict of forces.
def create_force_dict(system):
return {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
molecule_forces = create_force_dict(molecule_system)
forces = create_force_dict(system)
# Create Custom*Force classes if necessary.
if 'CustomBondForce' not in forces:
energy_expression = 'lambda*(K/2)*(r-length)^2;'
energy_expression += 'lambda = (1-alchemical_lambda)*delta(variant) + alchemical_lambda*delta(variant-alchemical_variant);'
custom_force = mm.CustomBondForce(energy_expression)
custom_force.addGlobalParameter('alchemical_lambda', 0.0)
custom_force.addGlobalParameter('alchemical_variant', 0.0)
custom_force.addPerBondParameter('variant')
custom_force.addPerBondParameter('length')
custom_force.addPerBondParameter('K')
system.addForce(custom_force)
forces['CustomBondForce'] = custom_force
if 'CustomAngleForce' not in forces:
energy_expression = 'lambda*(K/2)*(theta-theta0)^2;'
energy_expression += 'lambda = (1-alchemical_lambda)*delta(variant) + alchemical_lambda*delta(variant-alchemical_variant);'
custom_force = mm.CustomAngleForce(energy_expression)
custom_force.addGlobalParameter('alchemical_lambda', 0.0)
custom_force.addGlobalParameter('alchemical_variant', 0.0)
custom_force.addPerAngleParameter('variant')
custom_force.addPerAngleParameter('theta0')
custom_force.addPerAngleParameter('K')
system.addForce(custom_force)
forces['CustomAngleForce'] = custom_force
if 'CustomTorsionForce' not in forces:
energy_expression = 'lambda*K*(1+cos(periodicity*theta-phase));'
energy_expression += 'lambda = (1-alchemical_lambda)*delta(variant) + alchemical_lambda*delta(variant-alchemical_variant);'
custom_force = mm.CustomTorsionForce(energy_expression)
custom_force.addGlobalParameter('alchemical_lambda', 0.0)
custom_force.addGlobalParameter('alchemical_variant', 0.0)
custom_force.addPerTorsionParameter('variant')
custom_force.addPerTorsionParameter('periodicity')
custom_force.addPerTorsionParameter('phase')
custom_force.addPerTorsionParameter('K')
system.addForce(custom_force)
forces['CustomTorsionForce'] = custom_force
if 'CustomNonbondedForce' not in forces:
# DEBUG
# TODO: Create proper CustomNonbondedForce here.
energy_expression = "0.0;"
custom_force = mm.CustomNonbondedForce(energy_expression)
custom_force.addGlobalParameter('alchemical_lambda', 0.0)
custom_force.addGlobalParameter('alchemical_variant', 0.0)
custom_force.addPerParticleParameter('variant')
custom_force.addPerParticleParameter('charge')
custom_force.addPerParticleParameter('sigma')
custom_force.addPerParticleParameter('epsilon')
system.addForce(custom_force)
forces['CustomNonbondedForce'] = custom_force
# Add parameters for existing particles.
for index in range(system.getNumParticles()):
[charge, sigma,
epsilon] = forces['NonbondedForce'].getParticleParameters(index)
custom_force.addParticle([0, charge, sigma, epsilon])
# Add particles to system.
mapping = dict() # mapping[index_in_molecule] = index_in_system
for index_in_molecule in range(molecule_system.getNumParticles()):
# Add all atoms, unless we're adding the core, in which case we just add core atoms.
if (variant) or (index_in_molecule in core_atoms):
# TODO: We may want to make masses lighter.
index_in_system = system.addParticle(
system.getParticleMass(index_in_molecule))
mapping[index_in_molecule] = index_in_system
# Constraints are not supported.
# TODO: Later, consider supporting some constraints, such as those within core and those within variants.
if (molecule_system.getNumConstraints() > 0):
raise Exception(
"Constraints are not supported for alchemically modified molecule."
)
# Process forces.
# Valence terms involving only core atoms are created as Custom*Force classes where lambda=0 activates the "core" image and lambda=1 activates the "variant" image.
for (force_name, force) in molecule_forces.iteritems():
print force_name
if force_name == 'HarmonicBondForce':
for index in range(force.getNumBonds()):
[atom_i, atom_j, length, K] = force.getBondParameters(index)
if set([atom_i, atom_j]).issubset(core_atoms):
forces['CustomBondForce'].addBond(mapping[atom_i],
mapping[atom_j],
[variant, length, K])
elif (variant):
forces[force_name].addBond(mapping[atom_i],
mapping[atom_j], length, K)
elif force_name == 'HarmonicAngleForce':
for index in range(force.getNumAngles()):
[atom_i, atom_j, atom_k, theta0,
K] = force.getAngleParameters(index)
if set([atom_i, atom_j, atom_k]).issubset(core_atoms):
forces['CustomAngleForce'].addAngle(
mapping[atom_i], mapping[atom_j], mapping[atom_k],
[variant, theta0, K])
elif (variant):
forces[force_name].addAngle(mapping[atom_i],
mapping[atom_j],
mapping[atom_k], theta0, K)
elif force_name == 'PeriodicTorsionForce':
for index in range(force.getNumTorsions()):
[atom_i, atom_j, atom_k, atom_l, periodicity, phase,
K] = force.getTorsionParameters(index)
if set([atom_i, atom_j, atom_k, atom_l]).issubset(core_atoms):
forces['CustomTorsionForce'].addTorsion(
mapping[atom_i], mapping[atom_j], mapping[atom_k],
mapping[atom_l], [variant, periodicity, phase, K])
elif (variant):
forces[force_name].addTorsion(mapping[atom_i],
mapping[atom_j],
mapping[atom_k],
mapping[atom_l], periodicity,
phase, K)
elif force_name == 'NonbondedForce':
for index in range(force.getNumParticles()):
# TODO: Nonbonded terms will have to be handled as CustomNonbondedForce terms.
[charge, sigma, epsilon] = force.getParticleParameters(index)
if set([index]).issubset(core_atoms):
forces[force_name].addParticle(0.0 * charge, sigma,
0.0 * epsilon)
forces['CustomNonbondedForce'].addParticle(
[variant, charge, sigma, epsilon])
elif (variant):
forces[force_name].addParticle(0.0 * charge, sigma,
0.0 * epsilon)
forces['CustomNonbondedForce'].addParticle(
[variant, charge, sigma, epsilon])
for index in range(force.getNumExceptions()):
[atom_i, atom_j, chargeProd, sigma,
epsilon] = force.getExceptionParameters(index)
if set([atom_i, atom_j]).issubset(core_atoms):
# TODO: Nonbonded exceptions will have to be handled as CustomBondForce terms.
forces[force_name].addException(
mapping[atom_i], mapping[atom_j],
0.0 * unit.elementary_charge**2, 1.0 * unit.angstrom,
0.0 * unit.kilocalories_per_mole)
elif (variant):
forces[force_name].addException(mapping[atom_i],
mapping[atom_j],
chargeProd, sigma, epsilon)
# TODO: Add GB force processing.
# Add exclusions to previous variants and core.
for atom_i in mapping.values():
for atom_j in atoms_to_exclude:
forces['NonbondedForce'].addException(
atom_i, atom_j, 0.0 * unit.elementary_charge**2,
1.0 * unit.angstrom, 0.0 * unit.kilocalories_per_mole)
forces['CustomNonbondedForce'].addExclusion(atom_i, atom_j)
print system.getNumParticles(), forces['NonbondedForce'].getNumParticles()
return mapping
def redefine_angle(self,
topology,
residue,
atom1,
atom2,
atom3,
angle,
K=None,
group=1):
"""
Changes the equilibrium value of a specified angle for integration within its original
time scale. The difference between the original and the redefined angle potentials is
evaluated at another time scale.
Parameters
----------
topology : openmm.Topology
The topology corresponding to the original system.
residue : str
A name or regular expression to identify the residue which contains the redefined
angle.
atom1 : str
A name or regular expression to identify the first atom that makes the angle.
atom2 : str
A name or regular expression to identify the second atom that makes the angle.
atom3 : str
A name or regular expression to identify the third atom that makes the angle.
angle : unit.Quantity
The redifined equilibrium angle value for integration at the shortest time scale.
K : unit.Quantity, optional, default=None
The harmonic force constant for the angle. If this is `None`, then the original
value will be maintained.
group : int, optional, default=1
The force group with which the difference between the original and the redefined
angle potentials must be evaluated.
"""
resname = [atom.residue.name for atom in topology.atoms()]
atom = [atom.name for atom in topology.atoms()]
r_regex = re.compile(residue)
a_regex = [re.compile(a) for a in [atom1, atom2, atom3]]
def r_match(*args):
return all(r_regex.match(resname[j]) for j in args)
def a_match(*args):
return all(a_regex[i].match(atom[j]) for i, j in enumerate(args))
angle_list = []
for force in self.getForces():
if isinstance(force, openmm.HarmonicAngleForce):
for index in range(force.getNumAngles()):
i, j, k, theta0, K0 = force.getAngleParameters(index)
if r_match(i, j, k) and (a_match(i, j, k)
or a_match(k, j, i)):
force.setAngleParameters(index, i, j, k, angle,
K0 if K is None else K)
angle_list.append((i, j, k, theta0, K0))
if angle_list and self._special_angle_force is None:
new_force = openmm.CustomAngleForce(
'0.5*(K0*(theta - t0)^2 - Kn*(theta - tn)^2)')
new_force.addPerAngleParameter('t0')
new_force.addPerAngleParameter('K0')
new_force.addPerAngleParameter('tn')
new_force.addPerAngleParameter('Kn')
new_force.setForceGroup(group)
self.addForce(new_force)
self._special_angle_force = new_force
for (i, j, k, theta0, K0) in angle_list:
self._special_angle_force.addAngle(
i, j, k, (theta0, K0, angle, K0 if K is None else K))
def create_relative_alchemical_transformation(system, topology, positions, molecule1_indices_in_system, molecule1, molecule2,
softcore_alpha=0.5, softcore_beta=12*unit.angstrom**2):
"""
Create an OpenMM System object to handle the alchemical transformation from molecule1 to molecule2.
system : simtk.openmm.System
The system to be modified, already containing molecule1 whose atoms correspond to molecule1_indices_in_system.
topology : simtk.openmm.app.Topology
The topology object corresponding to system.
positions : simtk.unit.Quantity of numpy array natoms x 3 compatible with units angstroms
The positions array corresponding to system and topology.
molecule1_indices_in_system : list of int
Indices of molecule1 in system, with atoms in same order.
molecule1 : openeye.oechem.OEMol
Molecule already present in system, where the atom mapping is given by molecule1_indices_in_system.
molecule2 : openeye.oechem.OEMol
New molecule that molecule1 will be transformed into as lambda parameter goes from 0 -> 1.
softcore_alpha : float, optional, default=0.5
Softcore parameter for Lennard-Jones softening.
softcore_beta : simtk.unit.Quantity with units compatible with angstrom**2
Softcore parameter for Coulomb interaction softening.
Returns
-------
system : simtk.openmm.System
Modified version of system in which old system is recovered for global context paramaeter `lambda` = 0 and new molecule is substituted for `lambda` = 1.
topology : system.openmm.Topology
Topology corresponding to system.
"""
# Copy molecules.
molecule1 = oe.OEMol(molecule1)
molecule2 = oe.OEMol(molecule2)
# Normalize molecules.
# TODO: May need to do more normalization here.
oe.OEPerceiveChiral(molecule1)
oe.OEPerceiveChiral(molecule2)
# Make copies to not destroy original objects.
import copy
system = copy.deepcopy(system)
topology = copy.deepcopy(topology)
positions = copy.deepcopy(positions)
# Create lists of corresponding atoms for common substructure and groups specific to molecules 1 and 2.
atomexpr = oe.OEExprOpts_DefaultAtoms
bondexpr = oe.OEExprOpts_BondOrder | oe.OEExprOpts_EqSingleDouble | oe.OEExprOpts_EqAromatic
mcss = oe.OEMCSSearch(molecule1, atomexpr, bondexpr, oe.OEMCSType_Exhaustive)
# This modifies scoring function to prefer keeping cycles complete.
mcss.SetMCSFunc( oe.OEMCSMaxAtomsCompleteCycles() )
# TODO: Set initial substructure size?
# mcss.SetMinAtoms( some_number )
# We only need one match.
mcss.SetMaxMatches(1)
# Determine common atoms in second molecule.
matches = [ match for match in mcss.Match(molecule2, True) ]
match = matches[0] # we only need the first match
# Align common substructure of molecule2 with molecule1.
overlay = True
rmat = oe.OEDoubleArray(9)
trans = oe.OEDoubleArray(3)
rms = oe.OERMSD(mcss.GetPattern(), molecule2, match, overlay, rmat, trans)
if rms < 0.0:
raise Exception("RMS overlay failure")
oe.OERotate(molecule2, rmat)
oe.OETranslate(molecule2, trans)
# Make a list of the atoms in common, molecule1 only, and molecule2 only
common1 = list() # list of atom indices in molecule1 that also appear in molecule2
common2 = list() # list of atom indices in molecule2 that also appear in molecule1
unique1 = list() # list of atom indices in molecule1 that DO NOT appear in molecule2
unique2 = list() # list of atom indices in molecule2 that DO NOT appear in molecule1
mapping1 = dict() # mapping of atoms in molecule1 to molecule2
mapping2 = dict() # mapping of atoms in molecule2 to molecule1
for matchpair in match.GetAtoms():
index1 = matchpair.pattern.GetIdx()
index2 = matchpair.target.GetIdx()
mapping1[ index1 ] = index2
mapping2[ index2 ] = index1
all1 = frozenset(range(molecule1.NumAtoms()))
all2 = frozenset(range(molecule2.NumAtoms()))
common1 = frozenset(mapping1.keys())
common2 = frozenset(mapping2.keys())
unique1 = all1 - common1
unique2 = all2 - common2
# DEBUG
print "list of atoms common to both molecules:"
print "molecule1: %s" % str(common1)
print "molecule2: %s" % str(common2)
print "list of atoms unqiue to individual molecules:"
print "molecule1: %s" % str(unique1)
print "molecule2: %s" % str(unique2)
print "MAPPING FROM MOLECULE1 TO MOLECULE2"
for atom1 in mapping1.keys():
atom2 = mapping1[atom1]
print "%5d => %5d" % (atom1, atom2)
# Create OpenMM Topology and System objects for given molecules using GAFF/AM1-BCC.
# NOTE: This must generate the same forcefield parameters as occur in `system`.
[system1, topology1, positions1] = generate_openmm_system(molecule1)
[system2, topology2, positions2] = generate_openmm_system(molecule2)
#
# Start building combined OpenMM System object.
#
molecule1_atoms = [ atom for atom in molecule1.GetAtoms() ]
molecule2_atoms = [ atom for atom in molecule2.GetAtoms() ]
molecule2_indices_in_system = dict()
# Build mapping of common substructure for molecule 2.
for atom2 in common2:
molecule2_indices_in_system[atom2] = molecule1_indices_in_system[mapping2[atom2]]
# Find residue for molecule1.
residue = None
for atom in topology.atoms():
if atom.index in molecule1_indices_in_system:
residue = atom.residue
break
# Handle additional particles.
print "Adding particles from system2..."
for atom2 in unique2:
atom = molecule2_atoms[atom2]
name = atom.GetName()
atomic_number = atom.GetAtomicNum()
element = app.Element.getByAtomicNumber(atomic_number)
mass = system2.getParticleMass(atom2)
print [name, element, mass]
index = system.addParticle(mass)
molecule2_indices_in_system[atom2] = index
# TODO: Add new atoms to topology object as well.
topology.addAtom(name, element, residue)
# Turn molecule2_indices_in_system into list
molecule2_indices_in_system = [ molecule2_indices_in_system[atom2] for atom2 in range(molecule2.NumAtoms()) ]
print "Atom mappings into System object"
print "molecule1: %s" % str(molecule1_indices_in_system)
print "molecule2: %s" % str(molecule2_indices_in_system)
# Handle constraints.
# TODO: What happens if constraints change? Raise Exception then.
print "Adding constraints from system2..."
for index in range(system2.getNumConstraints()):
# Extract constraint distance from system2.
[atom2_i, atom2_j, distance] = system.getConstraintParameters(index)
# Map atoms from system2 into system.
atom_i = molecule2_indices_in_system[atom2_i]
atom_j = molecule2_indices_in_system[atom2_j]
# Add constraint to system.
system.addConstraint(atom_i, atom_j, distance)
# Create new positions array.
natoms = positions.shape[0] + len(unique2) # new number of atoms
positions = unit.Quantity(np.resize(positions/positions.unit, [natoms,3]), positions.unit)
for atom2 in unique2:
(x, y, z) = molecule2.GetCoords(molecule2_atoms[atom2])
index = molecule2_indices_in_system[atom2]
positions[index,0] = x * unit.angstrom
positions[index,1] = y * unit.angstrom
positions[index,2] = z * unit.angstrom
# Build a list of Force objects in system.
forces = [ system.getForce(index) for index in range(system.getNumForces()) ]
forces1 = { system1.getForce(index).__class__.__name__ : system1.getForce(index) for index in range(system1.getNumForces()) }
forces2 = { system2.getForce(index).__class__.__name__ : system2.getForce(index) for index in range(system2.getNumForces()) }
# Process forces.
for force in forces:
# Get force name.
force_name = force.__class__.__name__
force1 = forces1[force_name]
force2 = forces2[force_name]
print force_name
if force_name == 'HarmonicBondForce':
#
# Process HarmonicBondForce
#
# Create index of bonds in system, system1, and system2.
def unique(*args):
if args[0] > args[-1]:
return tuple(reversed(args))
else:
return tuple(args)
def index_bonds(force):
bonds = dict()
for index in range(force.getNumBonds()):
[atom_i, atom_j, length, K] = force.getBondParameters(index)
key = unique(atom_i, atom_j) # unique tuple, possibly in reverse order
bonds[key] = index
return bonds
bonds = index_bonds(force) # index of bonds for system
bonds1 = index_bonds(force1) # index of bonds for system1
bonds2 = index_bonds(force2) # index of bonds for system2
# Find bonds that are unique to each molecule.
print "Finding bonds unique to each molecule..."
unique_bonds1 = [ bonds1[atoms] for atoms in bonds1 if not set(atoms).issubset(common1) ]
unique_bonds2 = [ bonds2[atoms] for atoms in bonds2 if not set(atoms).issubset(common2) ]
# Build list of bonds shared among all molecules.
print "Building a list of shared bonds..."
shared_bonds = list()
for atoms2 in bonds2:
if set(atoms2).issubset(common2):
atoms = tuple(molecule2_indices_in_system[atom2] for atom2 in atoms2)
atoms1 = tuple(mapping2[atom2] for atom2 in atoms2)
# Find bond index terms.
index = bonds[unique(*atoms)]
index1 = bonds1[unique(*atoms1)]
index2 = bonds2[unique(*atoms2)]
# Store.
shared_bonds.append( (index, index1, index2) )
# Add bonds that are unique to molecule2.
print "Adding bonds unique to molecule2..."
for index2 in unique_bonds2:
[atom2_i, atom2_j, length2, K2] = force2.getBondParameters(index2)
atom_i = molecule2_indices_in_system[atom2_i]
atom_j = molecule2_indices_in_system[atom2_j]
force.addBond(atom_i, atom_j, length2, K2)
# Create a CustomBondForce to handle interpolated bond parameters.
print "Creating CustomBondForce..."
energy_expression = '(K/2)*(r-length)^2;'
energy_expression += 'K = (1-lambda)*K1 + lambda*K2;' # linearly interpolate spring constant
energy_expression += 'length = (1-lambda)*length1 + lambda*length2;' # linearly interpolate bond length
custom_force = mm.CustomBondForce(energy_expression)
custom_force.addGlobalParameter('lambda', 0.0)
custom_force.addPerBondParameter('length1') # molecule1 bond length
custom_force.addPerBondParameter('K1') # molecule1 spring constant
custom_force.addPerBondParameter('length2') # molecule2 bond length
custom_force.addPerBondParameter('K2') # molecule2 spring constant
system.addForce(custom_force)
# Process bonds that are shared by molecule1 and molecule2.
print "Translating shared bonds to CustomBondForce..."
for (index, index1, index2) in shared_bonds:
# Zero out standard bond force.
[atom_i, atom_j, length, K] = force.getBondParameters(index)
force.setBondParameters(index, atom_i, atom_j, length, K*0.0)
# Create interpolated bond parameters.
[atom1_i, atom1_j, length1, K1] = force1.getBondParameters(index1)
[atom2_i, atom2_j, length2, K2] = force2.getBondParameters(index2)
custom_force.addBond(atom_i, atom_j, [length1, K1, length2, K2])
if force_name == 'HarmonicAngleForce':
#
# Process HarmonicAngleForce
#
# Create index of angles in system, system1, and system2.
def unique(*args):
if args[0] > args[-1]:
return tuple(reversed(args))
else:
return tuple(args)
def index_angles(force):
angles = dict()
for index in range(force.getNumAngles()):
[atom_i, atom_j, atom_k, angle, K] = force.getAngleParameters(index)
key = unique(atom_i, atom_j, atom_k) # unique tuple, possibly in reverse order
angles[key] = index
return angles
angles = index_angles(force) # index of angles for system
angles1 = index_angles(force1) # index of angles for system1
angles2 = index_angles(force2) # index of angles for system2
# Find angles that are unique to each molecule.
print "Finding angles unique to each molecule..."
unique_angles1 = [ angles1[atoms] for atoms in angles1 if not set(atoms).issubset(common1) ]
unique_angles2 = [ angles2[atoms] for atoms in angles2 if not set(atoms).issubset(common2) ]
# Build list of angles shared among all molecules.
print "Building a list of shared angles..."
shared_angles = list()
for atoms2 in angles2:
if set(atoms2).issubset(common2):
atoms = tuple(molecule2_indices_in_system[atom2] for atom2 in atoms2)
atoms1 = tuple(mapping2[atom2] for atom2 in atoms2)
# Find angle index terms.
index = angles[unique(*atoms)]
index1 = angles1[unique(*atoms1)]
index2 = angles2[unique(*atoms2)]
# Store.
shared_angles.append( (index, index1, index2) )
# Add angles that are unique to molecule2.
print "Adding angles unique to molecule2..."
for index2 in unique_angles2:
[atom2_i, atom2_j, atom2_k, theta2, K2] = force2.getAngleParameters(index2)
atom_i = molecule2_indices_in_system[atom2_i]
atom_j = molecule2_indices_in_system[atom2_j]
atom_k = molecule2_indices_in_system[atom2_k]
force.addAngle(atom_i, atom_j, atom_k, theta2, K2)
# Create a CustomAngleForce to handle interpolated angle parameters.
print "Creating CustomAngleForce..."
energy_expression = '(K/2)*(theta-theta0)^2;'
energy_expression += 'K = (1-lambda)*K_1 + lambda*K_2;' # linearly interpolate spring constant
energy_expression += 'theta0 = (1-lambda)*theta0_1 + lambda*theta0_2;' # linearly interpolate equilibrium angle
custom_force = mm.CustomAngleForce(energy_expression)
custom_force.addGlobalParameter('lambda', 0.0)
custom_force.addPerAngleParameter('theta0_1') # molecule1 equilibrium angle
custom_force.addPerAngleParameter('K_1') # molecule1 spring constant
custom_force.addPerAngleParameter('theta0_2') # molecule2 equilibrium angle
custom_force.addPerAngleParameter('K_2') # molecule2 spring constant
system.addForce(custom_force)
# Process angles that are shared by molecule1 and molecule2.
print "Translating shared angles to CustomAngleForce..."
for (index, index1, index2) in shared_angles:
# Zero out standard angle force.
[atom_i, atom_j, atom_k, theta0, K] = force.getAngleParameters(index)
force.setAngleParameters(index, atom_i, atom_j, atom_k, theta0, K*0.0)
# Create interpolated angle parameters.
[atom1_i, atom1_j, atom1_k, theta1, K1] = force1.getAngleParameters(index1)
[atom2_i, atom2_j, atom2_k, theta2, K2] = force2.getAngleParameters(index2)
custom_force.addAngle(atom_i, atom_j, atom_k, [theta1, K1, theta2, K2])
if force_name == 'PeriodicTorsionForce':
#
# Process PeriodicTorsionForce
# TODO: Match up periodicities and deal with multiple terms per torsion
#
# Create index of torsions in system, system1, and system2.
def unique(*args):
if args[0] > args[-1]:
return tuple(reversed(args))
else:
return tuple(args)
def index_torsions(force):
torsions = dict()
for index in range(force.getNumTorsions()):
[atom_i, atom_j, atom_k, atom_l, periodicity, phase, K] = force.getTorsionParameters(index)
key = unique(atom_i, atom_j, atom_k, atom_l) # unique tuple, possibly in reverse order
torsions[key] = index
return torsions
torsions = index_torsions(force) # index of torsions for system
torsions1 = index_torsions(force1) # index of torsions for system1
torsions2 = index_torsions(force2) # index of torsions for system2
# Find torsions that are unique to each molecule.
print "Finding torsions unique to each molecule..."
unique_torsions1 = [ torsions1[atoms] for atoms in torsions1 if not set(atoms).issubset(common1) ]
unique_torsions2 = [ torsions2[atoms] for atoms in torsions2 if not set(atoms).issubset(common2) ]
# Build list of torsions shared among all molecules.
print "Building a list of shared torsions..."
shared_torsions = list()
for atoms2 in torsions2:
if set(atoms2).issubset(common2):
atoms = tuple(molecule2_indices_in_system[atom2] for atom2 in atoms2)
atoms1 = tuple(mapping2[atom2] for atom2 in atoms2)
# Find torsion index terms.
try:
index = torsions[unique(*atoms)]
index1 = torsions1[unique(*atoms1)]
index2 = torsions2[unique(*atoms2)]
except Exception as e:
print e
print "torsions : %s" % str(unique(*atoms))
print "torsions1: %s" % str(unique(*atoms1))
print "torsions2: %s" % str(unique(*atoms2))
raise Exception("Error occurred in building a list of torsions common to all molecules.")
# Store.
shared_torsions.append( (index, index1, index2) )
# Add torsions that are unique to molecule2.
print "Adding torsions unique to molecule2..."
for index2 in unique_torsions2:
[atom2_i, atom2_j, atom2_k, atom2_l, periodicity2, phase2, K2] = force2.getTorsionParameters(index2)
atom_i = molecule2_indices_in_system[atom2_i]
atom_j = molecule2_indices_in_system[atom2_j]
atom_k = molecule2_indices_in_system[atom2_k]
atom_l = molecule2_indices_in_system[atom2_l]
force.addTorsion(atom_i, atom_j, atom_k, atom_l, periodicity2, phase2, K2)
# Create a CustomTorsionForce to handle interpolated torsion parameters.
print "Creating CustomTorsionForce..."
energy_expression = '(1-lambda)*U1 + lambda*U2;'
energy_expression += 'U1 = K1*(1+cos(periodicity1*theta-phase1));'
energy_expression += 'U2 = K2*(1+cos(periodicity2*theta-phase2));'
custom_force = mm.CustomTorsionForce(energy_expression)
custom_force.addGlobalParameter('lambda', 0.0)
custom_force.addPerTorsionParameter('periodicity1') # molecule1 periodicity
custom_force.addPerTorsionParameter('phase1') # molecule1 phase
custom_force.addPerTorsionParameter('K1') # molecule1 spring constant
custom_force.addPerTorsionParameter('periodicity2') # molecule2 periodicity
custom_force.addPerTorsionParameter('phase2') # molecule2 phase
custom_force.addPerTorsionParameter('K2') # molecule2 spring constant
system.addForce(custom_force)
# Process torsions that are shared by molecule1 and molecule2.
print "Translating shared torsions to CustomTorsionForce..."
for (index, index1, index2) in shared_torsions:
# Zero out standard torsion force.
[atom_i, atom_j, atom_k, atom_l, periodicity, phase, K] = force.getTorsionParameters(index)
force.setTorsionParameters(index, atom_i, atom_j, atom_k, atom_l, periodicity, phase, K*0.0)
# Create interpolated torsion parameters.
[atom1_i, atom1_j, atom1_k, atom1_l, periodicity1, phase1, K1] = force1.getTorsionParameters(index1)
[atom2_i, atom2_j, atom2_k, atom2_l, periodicity2, phase2, K2] = force2.getTorsionParameters(index2)
custom_force.addTorsion(atom_i, atom_j, atom_k, atom_l, [periodicity1, phase1, K1, periodicity2, phase2, K2])
if force_name == 'NonbondedForce':
#
# Process NonbondedForce
#
# Add nonbonded entries for molecule2 to ensure total number of particle entries is correct.
for atom in unique2:
[charge, sigma, epsilon] = force2.getParticleParameters(atom)
force.addParticle(charge, sigma, epsilon)
# Zero out nonbonded entries for molecule1.
for atom in molecule1_indices_in_system:
[charge, sigma, epsilon] = force.getParticleParameters(atom)
force.setParticleParameters(atom, 0*charge, sigma, 0*epsilon)
# Zero out nonbonded entries for molecule2.
for atom in molecule2_indices_in_system:
[charge, sigma, epsilon] = force.getParticleParameters(atom)
force.setParticleParameters(atom, 0*charge, sigma, 0*epsilon)
# Create index of exceptions in system, system1, and system2.
def unique(*args):
if args[0] > args[-1]:
return tuple(reversed(args))
else:
return tuple(args)
def index_exceptions(force):
exceptions = dict()
for index in range(force.getNumExceptions()):
[atom_i, atom_j, chargeProd, sigma, epsilon] = force.getExceptionParameters(index)
key = unique(atom_i, atom_j) # unique tuple, possibly in reverse order
exceptions[key] = index
return exceptions
exceptions = index_exceptions(force) # index of exceptions for system
exceptions1 = index_exceptions(force1) # index of exceptions for system1
exceptions2 = index_exceptions(force2) # index of exceptions for system2
# Find exceptions that are unique to each molecule.
print "Finding exceptions unique to each molecule..."
unique_exceptions1 = [ exceptions1[atoms] for atoms in exceptions1 if not set(atoms).issubset(common1) ]
unique_exceptions2 = [ exceptions2[atoms] for atoms in exceptions2 if not set(atoms).issubset(common2) ]
# Build list of exceptions shared among all molecules.
print "Building a list of shared exceptions..."
shared_exceptions = list()
for atoms2 in exceptions2:
if set(atoms2).issubset(common2):
atoms = tuple(molecule2_indices_in_system[atom2] for atom2 in atoms2)
atoms1 = tuple(mapping2[atom2] for atom2 in atoms2)
# Find exception index terms.
index = exceptions[unique(*atoms)]
index1 = exceptions1[unique(*atoms1)]
index2 = exceptions2[unique(*atoms2)]
# Store.
shared_exceptions.append( (index, index1, index2) )
# Add exceptions that are unique to molecule2.
print "Adding exceptions unique to molecule2..."
for index2 in unique_exceptions2:
[atom2_i, atom2_j, chargeProd, sigma, epsilon] = force2.getExceptionParameters(index2)
atom_i = molecule2_indices_in_system[atom2_i]
atom_j = molecule2_indices_in_system[atom2_j]
force.addException(atom_i, atom_j, chargeProd, sigma, epsilon)
# Create list of alchemically modified atoms in system.
alchemical_atom_indices = list(set(molecule1_indices_in_system).union(set(molecule2_indices_in_system)))
# Create atom groups.
natoms = system.getNumParticles()
atomset1 = set(alchemical_atom_indices) # only alchemically-modified atoms
atomset2 = set(range(system.getNumParticles())) # all atoms, including alchemical region
# CustomNonbondedForce energy expression.
sterics_energy_expression = ""
electrostatics_energy_expression = ""
# Create a CustomNonbondedForce to handle alchemically interpolated nonbonded parameters.
# Select functional form based on nonbonded method.
method = force.getNonbondedMethod()
if method in [mm.NonbondedForce.NoCutoff]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = 4*epsilon*x*(x-1.0); x1 = (sigma/reff_sterics)^6;"
# soft-core Coulomb
electrostatics_energy_expression += "U_electrostatics = ONE_4PI_EPS0*chargeprod/reff_electrostatics;"
elif method in [mm.NonbondedForce.CutoffPeriodic, mm.NonbondedForce.CutoffNonPeriodic]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = 4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;"
# reaction-field electrostatics
epsilon_solvent = force.getReactionFieldDielectric()
r_cutoff = force.getCutoffDistance()
electrostatics_energy_expression += "U_electrostatics = ONE_4PI_EPS0*chargeprod*(reff_electrostatics^(-1) + k_rf*reff_electrostatics^2 - c_rf);"
k_rf = r_cutoff**(-3) * ((epsilon_solvent - 1) / (2*epsilon_solvent + 1))
c_rf = r_cutoff**(-1) * ((3*epsilon_solvent) / (2*epsilon_solvent + 1))
electrostatics_energy_expression += "k_rf = %f;" % (k_rf / k_rf.in_unit_system(unit.md_unit_system).unit)
electrostatics_energy_expression += "c_rf = %f;" % (c_rf / c_rf.in_unit_system(unit.md_unit_system).unit)
elif method in [mm.NonbondedForce.PME, mm.NonbondedForce.Ewald]:
# soft-core Lennard-Jones
sterics_energy_expression += "U_sterics = 4*epsilon*x*(x-1.0); x = (sigma/reff_sterics)^6;"
# Ewald direct-space electrostatics
[alpha_ewald, nx, ny, nz] = force.getPMEParameters()
if alpha_ewald == 0.0:
# If alpha is 0.0, alpha_ewald is computed by OpenMM from from the error tolerance.
delta = force.getEwaldErrorTolerance()
r_cutoff = force.getCutoffDistance()
alpha_ewald = np.sqrt(-np.log(2*delta)) / r_cutoff
electrostatics_energy_expression += "U_electrostatics = ONE_4PI_EPS0*chargeprod*erfc(alpha_ewald*reff_electrostatics)/reff_electrostatics;"
electrostatics_energy_expression += "alpha_ewald = %f;" % (alpha_ewald / alpha_ewald.in_unit_system(unit.md_unit_system).unit)
# TODO: Handle reciprocal-space electrostatics
else:
raise Exception("Nonbonded method %s not supported yet." % str(method))
# Add additional definitions common to all methods.
sterics_energy_expression += "epsilon = (1-lambda)*epsilonA + lambda*epsilonB;" #interpolation
sterics_energy_expression += "reff_sterics = sigma*((softcore_alpha*lambda_alpha + (r/sigma)^6))^(1/6);" # effective softcore distance for sterics
sterics_energy_expression += "softcore_alpha = %f;" % softcore_alpha
# TODO: We may have to ensure that softcore_degree is 1 if we are close to an alchemically-eliminated endpoint.
sterics_energy_expression += "lambda_alpha = lambda*(1-lambda);"
electrostatics_energy_expression += "chargeProd = (1-lambda)*chargeProdA + lambda*chargeProdB;" #interpolation
electrostatics_energy_expression += "reff_electrostatics = sqrt(softcore_beta*lambda_beta + r^2);" # effective softcore distance for electrostatics
electrostatics_energy_expression += "softcore_beta = %f;" % (softcore_beta / softcore_beta.in_unit_system(unit.md_unit_system).unit)
electrostatics_energy_expression += "ONE_4PI_EPS0 = %f;" % ONE_4PI_EPS0 # already in OpenMM units
# TODO: We may have to ensure that softcore_degree is 1 if we are close to an alchemically-eliminated endpoint.
sterics_energy_expression += "lambda_beta = lambda*(1-lambda);"
# Define mixing rules.
sterics_mixing_rules = ""
sterics_mixing_rules += "epsilonA = sqrt(epsilonA1*epsilonA2);" # mixing rule for epsilon
sterics_mixing_rules += "epsilonB = sqrt(epsilonB1*epsilonB2);" # mixing rule for epsilon
sterics_mixing_rules += "sigmaA = 0.5*(sigmaA1 + sigmaA2);" # mixing rule for sigma
sterics_mixing_rules += "sigmaB = 0.5*(sigmaB1 + sigmaB2);" # mixing rule for sigma
electrostatics_mixing_rules = ""
electrostatics_mixing_rules += "chargeprodA = chargeA1*chargeA2;" # mixing rule for charges
electrostatics_mixing_rules += "chargeprodB = chargeB1*chargeB2;" # mixing rule for charges
# Create CustomNonbondedForce to handle interactions between alchemically-modified atoms and rest of system.
electrostatics_custom_nonbonded_force = mm.CustomNonbondedForce("U_electrostatics;" + electrostatics_energy_expression + electrostatics_mixing_rules)
electrostatics_custom_nonbonded_force.addGlobalParameter("lambda", 0.0);
electrostatics_custom_nonbonded_force.addPerParticleParameter("chargeA") # partial charge initial
electrostatics_custom_nonbonded_force.addPerParticleParameter("chargeB") # partial charge final
sterics_custom_nonbonded_force = mm.CustomNonbondedForce("U_sterics;" + sterics_energy_expression + sterics_mixing_rules)
sterics_custom_nonbonded_force.addGlobalParameter("lambda", 0.0);
sterics_custom_nonbonded_force.addPerParticleParameter("sigmaA") # Lennard-Jones sigma initial
sterics_custom_nonbonded_force.addPerParticleParameter("epsilonA") # Lennard-Jones epsilon initial
sterics_custom_nonbonded_force.addPerParticleParameter("sigmaB") # Lennard-Jones sigma final
sterics_custom_nonbonded_force.addPerParticleParameter("epsilonB") # Lennard-Jones epsilon final
# Restrict interaction evaluation to be between alchemical atoms and rest of environment.
# TODO: Exclude intra-alchemical region if we are separately handling that through a separate CustomNonbondedForce for decoupling.
sterics_custom_nonbonded_force.addInteractionGroup(atomset1, atomset2)
electrostatics_custom_nonbonded_force.addInteractionGroup(atomset1, atomset2)
# Add exclusions between unique parts of molecule1 and molecule2 so they do not interact.
print "Add exclusions between unique parts of molecule1 and molecule2 that should not interact..."
for atom1_i in unique1:
for atom2_j in unique2:
atom_i = molecule1_indices_in_system[atom1_i]
atom_j = molecule2_indices_in_system[atom2_j]
electrostatics_custom_nonbonded_force.addExclusion(atom_i, atom_j)
sterics_custom_nonbonded_force.addExclusion(atom_i, atom_j)
# Add custom forces to system.
system.addForce(sterics_custom_nonbonded_force)
system.addForce(electrostatics_custom_nonbonded_force)
# Create CustomBondForce to handle exceptions for both kinds of interactions.
#custom_bond_force = mm.CustomBondForce("U_sterics + U_electrostatics;" + sterics_energy_expression + electrostatics_energy_expression)
#custom_bond_force.addGlobalParameter("lambda", 0.0);
#custom_bond_force.addPerBondParameter("chargeprodA") # charge product
#custom_bond_force.addPerBondParameter("sigmaA") # Lennard-Jones effective sigma
#custom_bond_force.addPerBondParameter("epsilonA") # Lennard-Jones effective epsilon
#custom_bond_force.addPerBondParameter("chargeprodB") # charge product
#custom_bond_force.addPerBondParameter("sigmaB") # Lennard-Jones effective sigma
#custom_bond_force.addPerBondParameter("epsilonB") # Lennard-Jones effective epsilon
#system.addForce(custom_bond_force)
# Copy over all Nonbonded parameters for normal atoms to Custom*Force objects.
for particle_index in range(force.getNumParticles()):
# Retrieve parameters.
[charge, sigma, epsilon] = force.getParticleParameters(particle_index)
# Add parameters to custom force handling interactions between alchemically-modified atoms and rest of system.
sterics_custom_nonbonded_force.addParticle([sigma, epsilon, sigma, epsilon])
electrostatics_custom_nonbonded_force.addParticle([charge, charge])
# Copy over parameters for common substructure.
for atom1 in common1:
atom2 = mapping1[atom1] # index into system2
index = molecule1_indices_in_system[atom1] # index into system
[charge1, sigma1, epsilon1] = force1.getParticleParameters(atom1)
[charge2, sigma2, epsilon2] = force2.getParticleParameters(atom2)
sterics_custom_nonbonded_force.setParticleParameters(index, [sigma1, epsilon1, sigma2, epsilon2])
electrostatics_custom_nonbonded_force.setParticleParameters(index, [charge1, charge2])
# Copy over parameters for molecule1 unique atoms.
for atom1 in unique1:
index = molecule1_indices_in_system[atom1] # index into system
[charge1, sigma1, epsilon1] = force1.getParticleParameters(atom1)
sterics_custom_nonbonded_force.setParticleParameters(index, [sigma1, epsilon1, sigma1, 0*epsilon1])
electrostatics_custom_nonbonded_force.setParticleParameters(index, [charge1, 0*charge1])
# Copy over parameters for molecule2 unique atoms.
for atom2 in unique2:
index = molecule2_indices_in_system[atom2] # index into system
[charge2, sigma2, epsilon2] = force2.getParticleParameters(atom2)
sterics_custom_nonbonded_force.setParticleParameters(index, [sigma2, 0*epsilon2, sigma2, epsilon2])
electrostatics_custom_nonbonded_force.setParticleParameters(index, [0*charge2, charge2])
else:
#raise Exception("Force type %s unknown." % force_name)
pass
return [system, topology, positions]
def apply_dat_restraint(system,
restraint,
phase,
window_number,
flat_bottom=False,
force_group=None):
"""A utility function which takes in pAPRika restraints and applies the
restraints to an OpenMM System object.
Parameters
----------
system : :class:`openmm.System`
The system object to add the positional restraints to.
restraint : list
List of pAPRika defined restraints
phase : str
Phase of calculation ("attach", "pull" or "release")
window_number : int
The corresponding window number of the current phase
flat_bottom : bool, optional
Specify whether the restraint is a flat bottom potential
force_group : int, optional
The force group to add the positional restraints to.
"""
from simtk import openmm, unit
assert phase in {"attach", "pull", "release"}
if flat_bottom and phase == "attach" and restraint.mask3:
flat_bottom_force = openmm.CustomAngleForce(
"step(-(theta - theta_0)) * k * (theta - theta_0)^2")
# If theta is greater than theta_0, then the argument to step is negative,
# which means the force is off.
flat_bottom_force.addPerAngleParameter("k")
flat_bottom_force.addPerAngleParameter("theta_0")
theta_0 = 91.0 * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
flat_bottom_force.addAngle(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
[k, theta_0],
)
system.addForce(flat_bottom_force)
if force_group:
flat_bottom_force.setForceGroup(force_group)
return
elif flat_bottom and phase == "attach" and not restraint.mask3:
flat_bottom_force = openmm.CustomBondForce(
"step((r - r_0)) * k * (r - r_0)^2")
# If x is greater than x_0, then the argument to step is positive, which means
# the force is on.
flat_bottom_force.addPerBondParameter("k")
flat_bottom_force.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][window_number] * unit.angstrom
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
flat_bottom_force.addBond(
restraint.index1[0],
restraint.index2[0],
[k, r_0],
)
system.addForce(flat_bottom_force)
if force_group:
flat_bottom_force.setForceGroup(force_group)
return
elif flat_bottom and phase == "pull":
return
elif flat_bottom and phase == "release":
return
if restraint.mask2 and not restraint.mask3:
if not restraint.group1 and not restraint.group2:
bond_restraint = openmm.CustomBondForce("k * (r - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][
window_number] * unit.angstroms
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.angstrom**2)
bond_restraint.addBond(restraint.index1[0], restraint.index2[0],
[k, r_0])
system.addForce(bond_restraint)
else:
bond_restraint = openmm.CustomCentroidBondForce(
2, "k * (distance(g1, g2) - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][
window_number] * unit.angstroms
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.angstrom**2)
g1 = bond_restraint.addGroup(restraint.index1)
g2 = bond_restraint.addGroup(restraint.index2)
bond_restraint.addBond([g1, g2], [k, r_0])
system.addForce(bond_restraint)
if force_group:
bond_restraint.setForceGroup(force_group)
elif restraint.mask3 and not restraint.mask4:
if not restraint.group1 and not restraint.group2 and not restraint.group3:
angle_restraint = openmm.CustomAngleForce(
"k * (theta - theta_0)^2")
angle_restraint.addPerAngleParameter("k")
angle_restraint.addPerAngleParameter("theta_0")
theta_0 = restraint.phase[phase]["targets"][
window_number] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
angle_restraint.addAngle(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
[k, theta_0],
)
system.addForce(angle_restraint)
else:
# Probably needs openmm.CustomCentroidAngleForce (?)
raise NotImplementedError
if force_group:
angle_restraint.setForceGroup(force_group)
elif restraint.mask4:
if (not restraint.group1 and not restraint.group2
and not restraint.group3 and not restraint.group4):
dihedral_restraint = openmm.CustomTorsionForce(
f"k * min(min(abs(theta - theta_0), abs(theta - theta_0 + 2 * "
f"{_PI_})), abs(theta - theta_0 - 2 * {_PI_}))^2")
dihedral_restraint.addPerTorsionParameter("k")
dihedral_restraint.addPerTorsionParameter("theta_0")
theta_0 = restraint.phase[phase]["targets"][
window_number] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
dihedral_restraint.addTorsion(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
restraint.index4[0],
[k, theta_0],
)
system.addForce(dihedral_restraint)
else:
# Probably needs openmm.CustomCentroidTorsionForce (?)
raise NotImplementedError
if force_group:
dihedral_restraint.setForceGroup(force_group)
def apply_openmm_restraints(system,
restraint,
window,
flat_bottom=False,
ForceGroup=None):
if window[0] == "a":
phase = "attach"
elif window[0] == "p":
phase = "pull"
elif window[0] == "r":
phase = "release"
window_number = int(window[1:])
if flat_bottom and phase == "attach" and restraint.mask3:
flat_bottom_force = openmm.CustomAngleForce(
'step(-(theta - theta_0)) * k * (theta - theta_0)^2')
# If theta is greater than theta_0, then the argument to step is negative, which means the force is off.
flat_bottom_force.addPerAngleParameter("k")
flat_bottom_force.addPerAngleParameter("theta_0")
theta_0 = 91.0 * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
flat_bottom_force.addAngle(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
[k, theta_0],
)
system.addForce(flat_bottom_force)
if ForceGroup:
flat_bottom_force.setForceGroup(ForceGroup)
return system
elif flat_bottom and phase == "attach" and not restraint.mask3:
flat_bottom_force = openmm.CustomBondForce(
'step((r - r_0)) * k * (r - r_0)^2')
# If x is greater than x_0, then the argument to step is positive, which means the force is on.
flat_bottom_force.addPerBondParameter("k")
flat_bottom_force.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][window_number] * unit.angstrom
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
flat_bottom_force.addBond(
restraint.index1[0],
restraint.index2[0],
[k, r_0],
)
system.addForce(flat_bottom_force)
if ForceGroup:
flat_bottom_force.setForceGroup(ForceGroup)
return system
elif flat_bottom and phase == "pull":
return system
elif flat_bottom and phase == "release":
return system
if restraint.mask2 and not restraint.mask3:
if not restraint.group1 and not restraint.group2:
bond_restraint = openmm.CustomBondForce("k * (r - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][
window_number] * unit.angstroms
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.angstrom**2)
bond_restraint.addBond(restraint.index1[0], restraint.index2[0],
[k, r_0])
system.addForce(bond_restraint)
else:
bond_restraint = openmm.CustomCentroidBondForce(
2, "k * (distance(g1, g2) - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][
window_number] * unit.angstroms
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.angstrom**2)
g1 = bond_restraint.addGroup(restraint.index1)
g2 = bond_restraint.addGroup(restraint.index2)
bond_restraint.addBond([g1, g2], [k, r_0])
system.addForce(bond_restraint)
if ForceGroup:
bond_restraint.setForceGroup(ForceGroup)
elif restraint.mask3 and not restraint.mask4:
if not restraint.group1 and not restraint.group2 and not restraint.group3:
angle_restraint = openmm.CustomAngleForce(
"k * (theta - theta_0)^2")
angle_restraint.addPerAngleParameter("k")
angle_restraint.addPerAngleParameter("theta_0")
theta_0 = restraint.phase[phase]["targets"][
window_number] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
angle_restraint.addAngle(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
[k, theta_0],
)
system.addForce(angle_restraint)
else:
# Probably needs openmm.CustomCentroidAngleForce (?)
raise NotImplementedError
if ForceGroup:
angle_restraint.setForceGroup(ForceGroup)
elif restraint.mask4:
if (not restraint.group1 and not restraint.group2
and not restraint.group3 and not restraint.group4):
dihedral_restraint = openmm.CustomTorsionForce(
f"k * min(min(abs(theta - theta_0), abs(theta - theta_0 + 2 * {_PI_})), abs(theta - theta_0 - 2 * {_PI_}))^2"
)
dihedral_restraint.addPerTorsionParameter("k")
dihedral_restraint.addPerTorsionParameter("theta_0")
theta_0 = restraint.phase[phase]["targets"][
window_number] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window_number] *
unit.kilocalories_per_mole / unit.radian**2)
dihedral_restraint.addTorsion(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
restraint.index4[0],
[k, theta_0],
)
system.addForce(dihedral_restraint)
else:
# Probably needs openmm.CustomCentroidTorsionForce (?)
raise NotImplementedError
if ForceGroup:
dihedral_restraint.setForceGroup(ForceGroup)
return system
def setup_openmm_restraints(system, restraint, phase, window):
"""
Add particle restraints with OpenMM.
"""
# http://docs.openmm.org/7.1.0/api-c++/generated/OpenMM.CustomExternalForce.html
# It's possible we might need to use `periodicdistance`.
if (restraint.mask1 is not None and restraint.mask2 is not None
and restraint.mask3 is None and restraint.mask4 is None):
if restraint.group1 is False and restraint.group2 is False:
bond_restraint = mm.CustomBondForce("k * (r - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][window] * unit.angstrom
k = (restraint.phase[phase]["force_constants"][window] *
unit.kilocalorie_per_mole / unit.angstrom**2)
bond_restraint.addBond(restraint.index1[0], restraint.index2[0],
[k, r_0])
bond_restraint.setForceGroup(1)
system.addForce(bond_restraint)
log.debug(
"Added bond restraint between {} and {} with target value = "
"{} and force constant = {}".format(restraint.mask1,
restraint.mask2, r_0, k))
elif restraint.group1 is True or restraint.group2 is True:
# http://docs.openmm.org/7.0.0/api-python/generated/simtk.openmm.openmm.CustomManyParticleForce.html
# http://getyank.org/development/_modules/yank/restraints.html
bond_restraint = mm.CustomCentroidBondForce(
2, "k * (distance(g1, g2) - r_0)^2")
bond_restraint.addPerBondParameter("k")
bond_restraint.addPerBondParameter("r_0")
r_0 = restraint.phase[phase]["targets"][window] * unit.angstrom
k = (restraint.phase[phase]["force_constants"][window] *
unit.kilocalorie_per_mole / unit.angstrom**2)
g1 = bond_restraint.addGroup(restraint.index1)
g2 = bond_restraint.addGroup(restraint.index2)
bond_restraint.addBond([g1, g2], [k, r_0])
bond_restraint.setForceGroup(1)
system.addForce(bond_restraint)
log.debug(
"Added bond restraint between {} and {} with target value = "
"{} and force constant = {}".format(restraint.mask1,
restraint.mask2, r_0, k))
else:
log.error("Unable to add bond restraint...")
log.debug("restraint.index1 = {}".format(restraint.index1))
log.debug("restraint.index2 = {}".format(restraint.index2))
raise Exception("Unable to add bond restraint...")
if (restraint.mask1 is not None and restraint.mask2 is not None
and restraint.mask3 is not None and restraint.mask4 is None):
if (restraint.group1 is not False and restraint.group2 is not False
and restraint.group3 is not False):
log.error("Unable to add a group angle restraint...")
log.debug("restraint.index1 = {}".format(restraint.index1))
log.debug("restraint.index2 = {}".format(restraint.index2))
log.debug("restraint.index3 = {}".format(restraint.index3))
raise Exception("Unable to add a group angle restraint...")
angle_restraint = mm.CustomAngleForce("k * (theta - theta_0)^2")
angle_restraint.addPerAngleParameter("k")
angle_restraint.addPerAngleParameter("theta_0")
log.debug("Setting an angle restraint in degrees using a "
"force constant in kcal per mol rad**2...")
theta_0 = restraint.phase[phase]["targets"][window] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window] *
unit.kilocalorie_per_mole / unit.radian**2)
angle_restraint.addAngle(restraint.index1[0], restraint.index2[0],
restraint.index3[0], [k, theta_0])
system.addForce(angle_restraint)
if (restraint.mask1 is not None and restraint.mask2 is not None
and restraint.mask3 is not None and restraint.mask4 is not None):
if (restraint.group1 is not False and restraint.group2 is not False
and restraint.group3 is not False
and restraint.group4 is not False):
log.error("Unable to add a group dihedral restraint...")
log.debug("restraint.index1 = {}".format(restraint.index1))
log.debug("restraint.index2 = {}".format(restraint.index2))
log.debug("restraint.index3 = {}".format(restraint.index3))
log.debug("restraint.index4 = {}".format(restraint.index4))
raise Exception("Unable to add a group dihedral restraint...")
dihedral_restraint = mm.CustomTorsionForce("k * (theta - theta_0)^2")
dihedral_restraint.addPerTorsionParameter("k")
dihedral_restraint.addPerTorsionParameter("theta_0")
log.debug("Setting a torsion restraint in degrees using a "
"force constant in kcal per mol rad**2...")
theta_0 = restraint.phase[phase]["targets"][window] * unit.degrees
k = (restraint.phase[phase]["force_constants"][window] *
unit.kilocalorie_per_mole / unit.radian**2)
dihedral_restraint.addTorsion(
restraint.index1[0],
restraint.index2[0],
restraint.index3[0],
restraint.index4[0],
[k, theta_0],
)
system.addForce(dihedral_restraint)
return system
