def _addVirtualSitesToSystem(self, sys):
"""Create any virtual sites in the systempy
"""
if not any(t.startswith('virtual_') for t in self._tables.keys()):
return
if 'virtual_lc2_term' in self._tables:
q = """SELECT p0, p1, p2, c1
FROM virtual_lc2_term INNER JOIN virtual_lc2_param
ON virtual_lc2_term.param=virtual_lc2_param.id"""
for p0, p1, p2, c1 in self._conn.execute(q):
vsite = mm.TwoParticleAverageSite(p1, p2, (1-c1), c1)
sys.setVirtualSite(p0, vsite)
if 'virtual_lc3_term' in self._tables:
q = """SELECT p0, p1, p2, p3, c1, c2
FROM virtual_lc3_term INNER JOIN virtual_lc3_param
ON virtual_lc3_term.param=virtual_lc3_param.id"""
for p0, p1, p2, p3, c1, c2 in self._conn.execute(q):
vsite = mm.ThreeParticleAverageSite(p1, p2, p3, (1-c1-c2), c1, c2)
sys.setVirtualSite(p0, vsite)
if 'virtual_out3_term' in self._tables:
q = """SELECT p0, p1, p2, p3, c1, c2, c3
FROM virtual_out3_term INNER JOIN virtual_out3_param
ON virtual_out3_term.param=virtual_out3_param.id"""
for p0, p1, p2, p3, c1, c2, c3 in self._conn.execute(q):
vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
sys.setVirtualSite(p0, vsite)
if 'virtual_fdat3_term' in self._tables:
raise NotImplementedError('OpenMM does not currently support '
'fdat3-style virtual sites')
def createSystem(self, topology, nonbondedMethod=NoCutoff,
nonbondedCutoff=1.0*u.nanometer, constraints=None,
rigidWater=True, removeCMMotion=True, hydrogenMass=None,
**args):
"""Construct an OpenMM System representing a Topology with this force field.
Parameters
----------
topology : Topology
The Topology for which to create a System
nonbondedMethod : object=NoCutoff
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
nonbondedCutoff : distance=1*nanometer
The cutoff distance to use for nonbonded interactions
constraints : object=None
Specifies which bonds and angles should be implemented with constraints.
Allowed values are None, HBonds, AllBonds, or HAngles.
rigidWater : boolean=True
If true, water molecules will be fully rigid regardless of the value
passed for the constraints argument
removeCMMotion : boolean=True
If true, a CMMotionRemover will be added to the System
hydrogenMass : mass=None
The mass to use for hydrogen atoms bound to heavy atoms. Any mass
added to a hydrogen is subtracted from the heavy atom to keep
their total mass the same.
args
Arbitrary additional keyword arguments may also be specified.
This allows extra parameters to be specified that are specific to
particular force fields.
Returns
-------
system
the newly created System
"""
# Atomtype the system.
G = nx.Graph()
G.add_nodes_from(topology.atoms())
G.add_edges_from(topology.bonds())
cycles = nx.cycle_basis(G)
for atom in topology.atoms():
atom.cycles = set()
for cycle in cycles:
for atom in cycle:
atom.cycles.add(tuple(cycle))
find_atomtypes(atoms=list(topology.atoms()), forcefield=self)
data = app.ForceField._SystemData()
data.atoms = list(topology.atoms())
for atom in data.atoms:
data.excludeAtomWith.append([])
# Make a list of all bonds
for bond in topology.bonds():
data.bonds.append(app.ForceField._BondData(bond[0].index, bond[1].index))
# Record which atoms are bonded to each other atom
bondedToAtom = []
for i in range(len(data.atoms)):
bondedToAtom.append(set())
data.atomBonds.append([])
for i in range(len(data.bonds)):
bond = data.bonds[i]
bondedToAtom[bond.atom1].add(bond.atom2)
bondedToAtom[bond.atom2].add(bond.atom1)
data.atomBonds[bond.atom1].append(i)
data.atomBonds[bond.atom2].append(i)
# TODO: Better way to lookup nonbonded parameters...?
nonbonded_params = None
for generator in self.getGenerators():
if isinstance(generator, NonbondedGenerator):
nonbonded_params = generator.params.paramsForType
break
for chain in topology.chains():
for res in chain.residues():
for atom in res.atoms():
data.atomType[atom] = atom.id
if nonbonded_params:
params = nonbonded_params[atom.id]
data.atomParameters[atom] = params
# Create the System and add atoms
sys = mm.System()
for atom in topology.atoms():
# Look up the atom type name, returning a helpful error message if it cannot be found.
if atom not in data.atomType:
raise Exception("Could not identify atom type for atom '%s'." % str(atom))
typename = data.atomType[atom]
# Look up the type name in the list of registered atom types, returning a helpful error message if it cannot be found.
if typename not in self._atomTypes:
msg = "Could not find typename '%s' for atom '%s' in list of known atom types.\n" % (typename, str(atom))
msg += "Known atom types are: %s" % str(self._atomTypes.keys())
raise Exception(msg)
# Add the particle to the OpenMM system.
mass = self._atomTypes[typename].mass
sys.addParticle(mass)
# Adjust hydrogen masses if requested.
if hydrogenMass is not None:
if not u.is_quantity(hydrogenMass):
hydrogenMass *= u.dalton
for atom1, atom2 in topology.bonds():
if atom1.element == elem.hydrogen:
(atom1, atom2) = (atom2, atom1)
if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None):
transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
sys.setParticleMass(atom2.index, hydrogenMass)
sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
# Set periodic boundary conditions.
boxVectors = topology.getPeriodicBoxVectors()
if boxVectors is not None:
sys.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2])
elif nonbondedMethod not in [NoCutoff, CutoffNonPeriodic]:
raise ValueError('Requested periodic boundary conditions for a Topology that does not specify periodic box dimensions')
# Make a list of all unique angles
uniqueAngles = set()
for bond in data.bonds:
for atom in bondedToAtom[bond.atom1]:
if atom != bond.atom2:
if atom < bond.atom2:
uniqueAngles.add((atom, bond.atom1, bond.atom2))
else:
uniqueAngles.add((bond.atom2, bond.atom1, atom))
for atom in bondedToAtom[bond.atom2]:
if atom != bond.atom1:
if atom > bond.atom1:
uniqueAngles.add((bond.atom1, bond.atom2, atom))
else:
uniqueAngles.add((atom, bond.atom2, bond.atom1))
data.angles = sorted(list(uniqueAngles))
# Make a list of all unique proper torsions
uniquePropers = set()
for angle in data.angles:
for atom in bondedToAtom[angle[0]]:
if atom not in angle:
if atom < angle[2]:
uniquePropers.add((atom, angle[0], angle[1], angle[2]))
else:
uniquePropers.add((angle[2], angle[1], angle[0], atom))
for atom in bondedToAtom[angle[2]]:
if atom not in angle:
if atom > angle[0]:
uniquePropers.add((angle[0], angle[1], angle[2], atom))
else:
uniquePropers.add((atom, angle[2], angle[1], angle[0]))
data.propers = sorted(list(uniquePropers))
# Make a list of all unique improper torsions
for atom in range(len(bondedToAtom)):
bondedTo = bondedToAtom[atom]
if len(bondedTo) > 2:
for subset in itertools.combinations(bondedTo, 3):
data.impropers.append((atom, subset[0], subset[1], subset[2]))
# Identify bonds that should be implemented with constraints
if constraints == AllBonds or constraints == HAngles:
for bond in data.bonds:
bond.isConstrained = True
elif constraints == HBonds:
for bond in data.bonds:
atom1 = data.atoms[bond.atom1]
atom2 = data.atoms[bond.atom2]
bond.isConstrained = atom1.name.startswith('H') or atom2.name.startswith('H')
if rigidWater:
for bond in data.bonds:
atom1 = data.atoms[bond.atom1]
atom2 = data.atoms[bond.atom2]
if atom1.residue.name == 'HOH' and atom2.residue.name == 'HOH':
bond.isConstrained = True
# Identify angles that should be implemented with constraints
if constraints == HAngles:
for angle in data.angles:
atom1 = data.atoms[angle[0]]
atom2 = data.atoms[angle[1]]
atom3 = data.atoms[angle[2]]
numH = 0
if atom1.name.startswith('H'):
numH += 1
if atom3.name.startswith('H'):
numH += 1
data.isAngleConstrained.append(numH == 2 or (numH == 1 and atom2.name.startswith('O')))
else:
data.isAngleConstrained = len(data.angles)*[False]
if rigidWater:
for i in range(len(data.angles)):
angle = data.angles[i]
atom1 = data.atoms[angle[0]]
atom2 = data.atoms[angle[1]]
atom3 = data.atoms[angle[2]]
if atom1.residue.name == 'HOH' and atom2.residue.name == 'HOH' and atom3.residue.name == 'HOH':
data.isAngleConstrained[i] = True
# Add virtual sites
for atom in data.virtualSites:
(site, atoms, excludeWith) = data.virtualSites[atom]
index = atom.index
data.excludeAtomWith[excludeWith].append(index)
if site.type == 'average2':
sys.setVirtualSite(index, mm.TwoParticleAverageSite(atoms[0], atoms[1], site.weights[0], site.weights[1]))
elif site.type == 'average3':
sys.setVirtualSite(index, mm.ThreeParticleAverageSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2]))
elif site.type == 'outOfPlane':
sys.setVirtualSite(index, mm.OutOfPlaneSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2]))
elif site.type == 'localCoords':
sys.setVirtualSite(index, mm.LocalCoordinatesSite(atoms[0], atoms[1], atoms[2],
mm.Vec3(site.originWeights[0], site.originWeights[1], site.originWeights[2]),
mm.Vec3(site.xWeights[0], site.xWeights[1], site.xWeights[2]),
mm.Vec3(site.yWeights[0], site.yWeights[1], site.yWeights[2]),
mm.Vec3(site.localPos[0], site.localPos[1], site.localPos[2])))
# Add forces to the System
for force in self._forces:
force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
if removeCMMotion:
sys.addForce(mm.CMMotionRemover())
# Let force generators do postprocessing
for force in self._forces:
if 'postprocessSystem' in dir(force):
force.postprocessSystem(sys, data, args)
# Execute scripts found in the XML files.
for script in self._scripts:
exec(script, locals())
return sys
def _addVirtualSitesToSystem(self, sys):
"""Create any virtual sites in the system
"""
go = []
for (fcounter, conn, tables, offset) in self._localVars():
if not any(t.startswith('virtual_') for t in list(tables.keys())):
go.append(False)
else:
go.append(True)
if not any(go):
return
for (fcounter, conn, tables, offset) in self._localVars():
if not go[fcounter]:
continue
if 'virtual_lc2_term' in tables:
q = """SELECT p0, p1, p2, c1
FROM virtual_lc2_term INNER JOIN virtual_lc2_param
ON virtual_lc2_term.param=virtual_lc2_param.id"""
for p0, p1, p2, c1 in conn.execute(q):
p0 += offset
p1 += offset
p2 += offset
vsite = mm.TwoParticleAverageSite(p1, p2, (1 - c1), c1)
sys.setVirtualSite(p0, vsite)
for (fcounter, conn, tables, offset) in self._localVars():
if not go[fcounter]:
continue
if 'virtual_lc3_term' in tables:
q = """SELECT p0, p1, p2, p3, c1, c2
FROM virtual_lc3_term INNER JOIN virtual_lc3_param
ON virtual_lc3_term.param=virtual_lc3_param.id"""
for p0, p1, p2, p3, c1, c2 in conn.execute(q):
p0 += offset
p1 += offset
p2 += offset
p3 += offset
vsite = mm.ThreeParticleAverageSite(
p1, p2, p3, (1 - c1 - c2), c1, c2)
sys.setVirtualSite(p0, vsite)
for (fcounter, conn, tables, offset) in self._localVars():
if not go[fcounter]:
continue
if 'virtual_out3_term' in tables:
q = """SELECT p0, p1, p2, p3, c1, c2, c3
FROM virtual_out3_term INNER JOIN virtual_out3_param
ON virtual_out3_term.param=virtual_out3_param.id"""
for p0, p1, p2, p3, c1, c2, c3 in conn.execute(q):
p0 += offset
p1 += offset
p2 += offset
p3 += offset
vsite = mm.OutOfPlaneSite(p1, p2, p3, c1, c2, c3)
sys.setVirtualSite(p0, vsite)
for (fcounter, conn, tables, offset) in self._localVars():
if not go[fcounter]:
continue
if 'virtual_fdat3_term' in tables:
raise NotImplementedError('OpenMM does not currently support '
'fdat3-style virtual sites')
def export(system):
'''
Generate OpenMM system from a system
Parameters
----------
system : System
Returns
-------
omm_system : simtk.openmm.System
'''
try:
import simtk.openmm as mm
except ImportError:
raise ImportError('Can not import OpenMM')
supported_terms = {
LJ126Term, MieTerm, HarmonicBondTerm, HarmonicAngleTerm,
SDKAngleTerm, PeriodicDihedralTerm, OplsImproperTerm,
HarmonicImproperTerm, DrudeTerm
}
unsupported = system.ff_classes - supported_terms
if unsupported != set():
raise Exception(
'Unsupported FF terms: %s' %
(', '.join(map(lambda x: x.__name__, unsupported))))
if system.vsite_types - {TIP4PSite} != set():
raise Exception(
'Virtual sites other than TIP4PSite haven\'t been implemented')
top = system.topology
ff = system.ff
omm_system = mm.System()
if system.use_pbc:
omm_system.setDefaultPeriodicBoxVectors(*top.cell.vectors)
for atom in top.atoms:
omm_system.addParticle(atom.mass)
### Set up bonds #######################################################################
for bond_class in system.bond_classes:
if bond_class == HarmonicBondTerm:
logger.info('Setting up harmonic bonds...')
bforce = mm.HarmonicBondForce()
for bond in top.bonds:
if bond.is_drude:
# DrudeForce will handle the bond between Drude pair
continue
bterm = system.bond_terms[id(bond)]
if type(bterm) != HarmonicBondTerm:
continue
bforce.addBond(bond.atom1.id, bond.atom2.id, bterm.length,
bterm.k * 2)
else:
raise Exception('Bond terms other that HarmonicBondTerm '
'haven\'t been implemented')
bforce.setUsesPeriodicBoundaryConditions(system.use_pbc)
bforce.setForceGroup(ForceGroup.BOND)
omm_system.addForce(bforce)
### Set up angles #######################################################################
for angle_class in system.angle_classes:
if angle_class == HarmonicAngleTerm:
logger.info('Setting up harmonic angles...')
aforce = mm.HarmonicAngleForce()
for angle in top.angles:
aterm = system.angle_terms[id(angle)]
if type(aterm) == HarmonicAngleTerm:
aforce.addAngle(angle.atom1.id, angle.atom2.id,
angle.atom3.id, aterm.theta * PI / 180,
aterm.k * 2)
elif angle_class == SDKAngleTerm:
logger.info('Setting up SDK angles...')
aforce = mm.CustomCompoundBondForce(
3, 'k*(theta-theta0)^2+step(rmin-r)*LJ96;'
'LJ96=6.75*epsilon*((sigma/r)^9-(sigma/r)^6)+epsilon;'
'theta=angle(p1,p2,p3);'
'r=distance(p1,p3);'
'rmin=1.144714*sigma')
aforce.addPerBondParameter('theta0')
aforce.addPerBondParameter('k')
aforce.addPerBondParameter('epsilon')
aforce.addPerBondParameter('sigma')
for angle in top.angles:
aterm = system.angle_terms[id(angle)]
if type(aterm) != SDKAngleTerm:
continue
vdw = ff.get_vdw_term(ff.atom_types[angle.atom1.type],
ff.atom_types[angle.atom2.type])
if type(
vdw
) != MieTerm or vdw.repulsion != 9 or vdw.attraction != 6:
raise Exception(
f'Corresponding 9-6 MieTerm for {aterm} not found in FF'
)
aforce.addBond(
[angle.atom1.id, angle.atom2.id, angle.atom3.id], [
aterm.theta * PI / 180, aterm.k, vdw.epsilon,
vdw.sigma
])
else:
raise Exception(
'Angle terms other that HarmonicAngleTerm and SDKAngleTerm '
'haven\'t been implemented')
aforce.setUsesPeriodicBoundaryConditions(system.use_pbc)
aforce.setForceGroup(ForceGroup.ANGLE)
omm_system.addForce(aforce)
### Set up constraints #################################################################
logger.info(
f'Setting up {len(system.constrain_bonds)} bond constraints...')
for bond in top.bonds:
if id(bond) in system.constrain_bonds:
omm_system.addConstraint(bond.atom1.id, bond.atom2.id,
system.constrain_bonds[id(bond)])
logger.info(
f'Setting up {len(system.constrain_angles)} angle constraints...')
for angle in top.angles:
if id(angle) in system.constrain_angles:
omm_system.addConstraint(angle.atom1.id, angle.atom3.id,
system.constrain_angles[id(angle)])
### Set up dihedrals ###################################################################
for dihedral_class in system.dihedral_classes:
if dihedral_class == PeriodicDihedralTerm:
logger.info('Setting up periodic dihedrals...')
dforce = mm.PeriodicTorsionForce()
for dihedral in top.dihedrals:
dterm = system.dihedral_terms[id(dihedral)]
ia1, ia2, ia3, ia4 = dihedral.atom1.id, dihedral.atom2.id, dihedral.atom3.id, dihedral.atom4.id
if type(dterm) == PeriodicDihedralTerm:
for par in dterm.parameters:
dforce.addTorsion(ia1, ia2, ia3, ia4, par.n,
par.phi * PI / 180, par.k)
else:
continue
else:
raise Exception(
'Dihedral terms other that PeriodicDihedralTerm '
'haven\'t been implemented')
dforce.setUsesPeriodicBoundaryConditions(system.use_pbc)
dforce.setForceGroup(ForceGroup.DIHEDRAL)
omm_system.addForce(dforce)
### Set up impropers ####################################################################
for improper_class in system.improper_classes:
if improper_class == OplsImproperTerm:
logger.info('Setting up periodic impropers...')
iforce = mm.CustomTorsionForce('k*(1-cos(2*theta))')
iforce.addPerTorsionParameter('k')
for improper in top.impropers:
iterm = system.improper_terms[id(improper)]
if type(iterm) == OplsImproperTerm:
# in OPLS convention, the third atom is the central atom
iforce.addTorsion(improper.atom2.id, improper.atom3.id,
improper.atom1.id, improper.atom4.id,
[iterm.k])
elif improper_class == HarmonicImproperTerm:
logger.info('Setting up harmonic impropers...')
iforce = mm.CustomTorsionForce(f'k*min(dtheta,2*pi-dtheta)^2;'
f'dtheta=abs(theta-phi0);'
f'pi={PI}')
iforce.addPerTorsionParameter('phi0')
iforce.addPerTorsionParameter('k')
for improper in top.impropers:
iterm = system.improper_terms[id(improper)]
if type(iterm) == HarmonicImproperTerm:
iforce.addTorsion(improper.atom1.id, improper.atom2.id,
improper.atom3.id, improper.atom4.id,
[iterm.phi * PI / 180, iterm.k])
else:
raise Exception(
'Improper terms other that PeriodicImproperTerm and '
'HarmonicImproperTerm haven\'t been implemented')
iforce.setUsesPeriodicBoundaryConditions(system.use_pbc)
iforce.setForceGroup(ForceGroup.IMPROPER)
omm_system.addForce(iforce)
### Set up non-bonded interactions #########################################################
# NonbonedForce is not flexible enough. Use it only for Coulomb interactions (including 1-4 Coulomb exceptions)
# CustomNonbondedForce handles vdW interactions (including 1-4 LJ exceptions)
cutoff = ff.vdw_cutoff
logger.info('Setting up Coulomb interactions...')
nbforce = mm.NonbondedForce()
if system.use_pbc:
nbforce.setNonbondedMethod(mm.NonbondedForce.PME)
nbforce.setEwaldErrorTolerance(5E-4)
nbforce.setCutoffDistance(cutoff)
# dispersion will be handled by CustomNonbondedForce
nbforce.setUseDispersionCorrection(False)
try:
nbforce.setExceptionsUsePeriodicBoundaryConditions(True)
except:
logger.warning('Cannot apply PBC for Coulomb 1-4 exceptions')
else:
nbforce.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
nbforce.setForceGroup(ForceGroup.COULOMB)
omm_system.addForce(nbforce)
for atom in top.atoms:
nbforce.addParticle(atom.charge, 1.0, 0.0)
### Set up vdW interactions #########################################################
atom_types = list(ff.atom_types.values())
type_names = list(ff.atom_types.keys())
n_type = len(atom_types)
for vdw_class in system.vdw_classes:
if vdw_class == LJ126Term:
logger.info('Setting up LJ-12-6 vdW interactions...')
if system.use_pbc and ff.vdw_long_range == ForceField.VDW_LONGRANGE_SHIFT:
invRc6 = 1 / cutoff**6
cforce = mm.CustomNonbondedForce(
f'A(type1,type2)*(invR6*invR6-{invRc6 * invRc6})-'
f'B(type1,type2)*(invR6-{invRc6});'
f'invR6=1/r^6')
else:
cforce = mm.CustomNonbondedForce(
'A(type1,type2)*invR6*invR6-B(type1,type2)*invR6;'
'invR6=1/r^6')
cforce.addPerParticleParameter('type')
A_list = [0.0] * n_type * n_type
B_list = [0.0] * n_type * n_type
for i, atype1 in enumerate(atom_types):
for j, atype2 in enumerate(atom_types):
vdw = ff.get_vdw_term(atype1, atype2)
if type(vdw) == LJ126Term:
A = 4 * vdw.epsilon * vdw.sigma**12
B = 4 * vdw.epsilon * vdw.sigma**6
else:
A = B = 0
A_list[i + n_type * j] = A
B_list[i + n_type * j] = B
cforce.addTabulatedFunction(
'A', mm.Discrete2DFunction(n_type, n_type, A_list))
cforce.addTabulatedFunction(
'B', mm.Discrete2DFunction(n_type, n_type, B_list))
for atom in top.atoms:
id_type = type_names.index(atom.type)
cforce.addParticle([id_type])
elif vdw_class == MieTerm:
logger.info('Setting up Mie vdW interactions...')
if system.use_pbc and ff.vdw_long_range == ForceField.VDW_LONGRANGE_SHIFT:
cforce = mm.CustomNonbondedForce(
'A(type1,type2)/r^REP(type1,type2)-'
'B(type1,type2)/r^ATT(type1,type2)-'
'SHIFT(type1,type2)')
else:
cforce = mm.CustomNonbondedForce(
'A(type1,type2)/r^REP(type1,type2)-'
'B(type1,type2)/r^ATT(type1,type2)')
cforce.addPerParticleParameter('type')
A_list = [0.0] * n_type * n_type
B_list = [0.0] * n_type * n_type
REP_list = [0.0] * n_type * n_type
ATT_list = [0.0] * n_type * n_type
SHIFT_list = [0.0] * n_type * n_type
for i, atype1 in enumerate(atom_types):
for j, atype2 in enumerate(atom_types):
vdw = ff.get_vdw_term(atype1, atype2)
if type(vdw) == MieTerm:
A = vdw.factor_energy(
) * vdw.epsilon * vdw.sigma**vdw.repulsion
B = vdw.factor_energy(
) * vdw.epsilon * vdw.sigma**vdw.attraction
REP = vdw.repulsion
ATT = vdw.attraction
SHIFT = A / cutoff**REP - B / cutoff**ATT
else:
A = B = REP = ATT = SHIFT = 0
A_list[i + n_type * j] = A
B_list[i + n_type * j] = B
REP_list[i + n_type * j] = REP
ATT_list[i + n_type * j] = ATT
SHIFT_list[i + n_type * j] = SHIFT
cforce.addTabulatedFunction(
'A', mm.Discrete2DFunction(n_type, n_type, A_list))
cforce.addTabulatedFunction(
'B', mm.Discrete2DFunction(n_type, n_type, B_list))
cforce.addTabulatedFunction(
'REP', mm.Discrete2DFunction(n_type, n_type, REP_list))
cforce.addTabulatedFunction(
'ATT', mm.Discrete2DFunction(n_type, n_type, ATT_list))
if system.use_pbc and ff.vdw_long_range == ForceField.VDW_LONGRANGE_SHIFT:
cforce.addTabulatedFunction(
'SHIFT',
mm.Discrete2DFunction(n_type, n_type, SHIFT_list))
for atom in top.atoms:
id_type = type_names.index(atom.type)
cforce.addParticle([id_type])
else:
raise Exception('vdW terms other than LJ126Term and MieTerm '
'haven\'t been implemented')
if system.use_pbc:
cforce.setNonbondedMethod(
mm.CustomNonbondedForce.CutoffPeriodic)
cforce.setCutoffDistance(cutoff)
if ff.vdw_long_range == ForceField.VDW_LONGRANGE_CORRECT:
cforce.setUseLongRangeCorrection(True)
else:
cforce.setNonbondedMethod(mm.CustomNonbondedForce.NoCutoff)
cforce.setForceGroup(ForceGroup.VDW)
omm_system.addForce(cforce)
### Set up 1-2, 1-3 and 1-4 exceptions ##################################################
logger.info('Setting up 1-2, 1-3 and 1-4 exceptions...')
custom_nb_forces = [
f for f in omm_system.getForces()
if type(f) == mm.CustomNonbondedForce
]
pair12, pair13, pair14 = top.get_12_13_14_pairs()
for atom1, atom2 in pair12 + pair13:
nbforce.addException(atom1.id, atom2.id, 0.0, 1.0, 0.0)
for f in custom_nb_forces:
f.addExclusion(atom1.id, atom2.id)
# As long as 1-4 LJ OR Coulomb need to be scaled, then this pair should be excluded from ALL non-bonded forces.
# This is required by OpenMM's internal implementation.
# Even though NonbondedForce can handle 1-4 vdW, we use it only for 1-4 Coulomb.
# And use CustomBondForce to handle 1-4 vdW, which makes it more clear for energy decomposition.
if ff.scale_14_vdw != 1 or ff.scale_14_coulomb != 1:
pair14_forces = {} # {VdwTerm: mm.NbForce}
for atom1, atom2 in pair14:
charge_prod = atom1.charge * atom2.charge * ff.scale_14_coulomb
nbforce.addException(atom1.id, atom2.id, charge_prod, 1.0, 0.0)
for f in custom_nb_forces:
f.addExclusion(atom1.id, atom2.id)
if ff.scale_14_vdw == 0:
continue
vdw = ff.get_vdw_term(ff.atom_types[atom1.type],
ff.atom_types[atom2.type])
# We generalize LJ126Term and MieTerm because of minimal computational cost for 1-4 vdW
if type(vdw) in (LJ126Term, MieTerm):
cbforce = pair14_forces.get(MieTerm)
if cbforce is None:
cbforce = mm.CustomBondForce(
'C*epsilon*((sigma/r)^n-(sigma/r)^m);'
'C=n/(n-m)*(n/m)^(m/(n-m))')
cbforce.addPerBondParameter('epsilon')
cbforce.addPerBondParameter('sigma')
cbforce.addPerBondParameter('n')
cbforce.addPerBondParameter('m')
cbforce.setUsesPeriodicBoundaryConditions(
system.use_pbc)
cbforce.setForceGroup(ForceGroup.VDW)
omm_system.addForce(cbforce)
pair14_forces[MieTerm] = cbforce
epsilon = vdw.epsilon * ff.scale_14_vdw
if type(vdw) == LJ126Term:
cbforce.addBond(atom1.id, atom2.id,
[epsilon, vdw.sigma, 12, 6])
elif type(vdw) == MieTerm:
cbforce.addBond(atom1.id, atom2.id, [
epsilon, vdw.sigma, vdw.repulsion, vdw.attraction
])
else:
raise Exception(
'1-4 scaling for vdW terms other than LJ126Term and MieTerm '
'haven\'t been implemented')
### Set up Drude particles ##############################################################
for polar_class in system.polarizable_classes:
if polar_class == DrudeTerm:
logger.info('Setting up Drude polarizations...')
pforce = mm.DrudeForce()
pforce.setForceGroup(ForceGroup.DRUDE)
omm_system.addForce(pforce)
parent_idx_thole = {
} # {parent: (index in DrudeForce, thole)} for addScreenPair
for parent, drude in system.drude_pairs.items():
pterm = system.polarizable_terms[parent]
n_H = len([
atom for atom in parent.bond_partners
if atom.symbol == 'H'
])
alpha = pterm.alpha + n_H * pterm.merge_alpha_H
idx = pforce.addParticle(drude.id, parent.id, -1, -1, -1,
drude.charge, alpha, 0, 0)
parent_idx_thole[parent] = (idx, pterm.thole)
# exclude the non-boned interactions between Drude and parent
# and those concerning Drude particles in 1-2 and 1-3 pairs
# pairs formed by real atoms have already been handled above
# also apply thole screening between 1-2 and 1-3 Drude dipole pairs
drude_exclusions = list(system.drude_pairs.items())
for atom1, atom2 in pair12 + pair13:
drude1 = system.drude_pairs.get(atom1)
drude2 = system.drude_pairs.get(atom2)
if drude1 is not None:
drude_exclusions.append((drude1, atom2))
if drude2 is not None:
drude_exclusions.append((atom1, drude2))
if drude1 is not None and drude2 is not None:
drude_exclusions.append((drude1, drude2))
idx1, thole1 = parent_idx_thole[atom1]
idx2, thole2 = parent_idx_thole[atom2]
pforce.addScreenedPair(idx1, idx2,
(thole1 + thole2) / 2)
for a1, a2 in drude_exclusions:
nbforce.addException(a1.id, a2.id, 0, 1.0, 0)
for f in custom_nb_forces:
f.addExclusion(a1.id, a2.id)
# scale the non-boned interactions concerning Drude particles in 1-4 pairs
# pairs formed by real atoms have already been handled above
drude_exceptions14 = []
for atom1, atom2 in pair14:
drude1 = system.drude_pairs.get(atom1)
drude2 = system.drude_pairs.get(atom2)
if drude1 is not None:
drude_exceptions14.append((drude1, atom2))
if drude2 is not None:
drude_exceptions14.append((atom1, drude2))
if drude1 is not None and drude2 is not None:
drude_exceptions14.append((drude1, drude2))
for a1, a2 in drude_exceptions14:
charge_prod = a1.charge * a2.charge * ff.scale_14_coulomb
nbforce.addException(a1.id, a2.id, charge_prod, 1.0, 0.0)
for f in custom_nb_forces:
f.addExclusion(a1.id, a2.id)
else:
raise Exception(
'Polarizable terms other that DrudeTerm haven\'t been implemented'
)
### Set up virtual sites ################################################################
if top.has_virtual_site:
logger.info('Setting up virtual sites...')
for atom in top.atoms:
vsite = atom.virtual_site
if type(vsite) == TIP4PSite:
O, H1, H2 = vsite.parents
coeffs = system.get_TIP4P_linear_coeffs(atom)
omm_vsite = mm.ThreeParticleAverageSite(
O.id, H1.id, H2.id, *coeffs)
omm_system.setVirtualSite(atom.id, omm_vsite)
elif vsite is not None:
raise Exception(
'Virtual sites other than TIP4PSite haven\'t been implemented'
)
# exclude the non-boned interactions between virtual sites and parents
# and particles (atoms, drude particles, virtual sites) in 1-2 and 1-3 pairs
# TODO Assume no more than one virtual site is attached to each atom
vsite_exclusions = list(system.vsite_pairs.items())
for atom, vsite in system.vsite_pairs.items():
drude = system.drude_pairs.get(atom)
if drude is not None:
vsite_exclusions.append((vsite, drude))
for atom1, atom2 in pair12 + pair13:
vsite1 = system.vsite_pairs.get(atom1)
vsite2 = system.vsite_pairs.get(atom2)
drude1 = system.drude_pairs.get(atom1)
drude2 = system.drude_pairs.get(atom2)
if vsite1 is not None:
vsite_exclusions.append((vsite1, atom2))
if drude2 is not None:
vsite_exclusions.append((vsite1, drude2))
if vsite2 is not None:
vsite_exclusions.append((vsite2, atom1))
if drude1 is not None:
vsite_exclusions.append((vsite2, drude1))
if None not in [vsite1, vsite2]:
vsite_exclusions.append((vsite1, vsite2))
for a1, a2 in vsite_exclusions:
nbforce.addException(a1.id, a2.id, 0, 1.0, 0)
for f in custom_nb_forces:
f.addExclusion(a1.id, a2.id)
# scale the non-boned interactions between virtual sites and particles in 1-4 pairs
# TODO Assume no 1-4 LJ interactions on virtual sites
vsite_exceptions14 = []
for atom1, atom2 in pair14:
vsite1 = system.vsite_pairs.get(atom1)
vsite2 = system.vsite_pairs.get(atom2)
drude1 = system.drude_pairs.get(atom1)
drude2 = system.drude_pairs.get(atom2)
if vsite1 is not None:
vsite_exceptions14.append((vsite1, atom2))
if drude2 is not None:
vsite_exceptions14.append((vsite1, drude2))
if vsite2 is not None:
vsite_exceptions14.append((vsite2, atom1))
if drude1 is not None:
vsite_exceptions14.append((vsite2, drude1))
if None not in [vsite1, vsite2]:
vsite_exceptions14.append((vsite1, vsite2))
for a1, a2 in vsite_exceptions14:
charge_prod = a1.charge * a2.charge * ff.scale_14_coulomb
nbforce.addException(a1.id, a2.id, charge_prod, 1.0, 0.0)
for f in custom_nb_forces:
f.addExclusion(a1.id, a2.id)
### Remove COM motion ###################################################################
logger.info('Setting up COM motion remover...')
omm_system.addForce(mm.CMMotionRemover(10))
return omm_system
