def get_openmm_integrator(self):
from simtk import openmm
integrator = openmm.LangevinIntegrator(
pint2simtk(self.params.temperature),
pint2simtk(self.params.collision_rate),
pint2simtk(self.params.timestep))
return integrator
def _set_constraints(self):
system = self.mm_system
fixed_atoms = set()
# Constrain atom positions
for constraint in self.mol.constraints:
if constraint.desc == 'position':
fixed_atoms.add(constraint.atom)
self.mol.assert_atom(constraint.atom)
system.setParticleMass(constraint.atom.index, 0.0)
# Constrain distances between atom pairs
elif constraint.desc == 'distance':
self.mol.assert_atom(constraint.a1)
self.mol.assert_atom(constraint.a2)
system.addConstraint(constraint.a1,
constraint.a2,
opm.pint2simtk(constraint.value))
else:
raise ValueError('OpenMM interface does not support "%s" constraints.' % constraint.desc)
# Workaround for OpenMM issue: can't have an atom that's both fixed *and* has a distance constraint.
# If both atoms in the distance constraint are also fixed, then we can just remove the constraint
if len(fixed_atoms) > 0:
num_constraints = system.getNumConstraints()
ic = 0
while ic < num_constraints:
i, j, dist = system.getConstraintParameters(ic)
ai = self.mol.atoms[i]
aj = self.mol.atoms[j]
if (ai in fixed_atoms) and (aj in fixed_atoms):
system.removeConstraint(ic)
num_constraints -= 1
elif (ai in fixed_atoms) or (aj in fixed_atoms): #only one is fixed
raise ValueError('In OpenMM, fixed atoms cannot be part of a constrained '
'bond (%s)'%moldesign.molecules.bonds.Bond(ai, aj))
else:
ic += 1
def _get_system_params(self):
""" Translates the spec from MMBase into system parameter keywords for createSystem
"""
# need cmm motion
nonbonded_names = {'nocutoff': opm.app.NoCutoff,
'ewald': opm.app.Ewald,
'pme': opm.app.PME,
'cutoff': opm.app.CutoffPeriodic if self.params.periodic else opm.app.CutoffNonPeriodic}
implicit_solvent_names = {'obc': opm.app.OBC2}
system_params = dict(nonbondedMethod=nonbonded_names[self.params.nonbonded],
nonbondedCutoff=opm.pint2simtk(self.params.cutoff),
implicitSolvent=implicit_solvent_names[self.params.implicit_solvent])
system_params['rigidWater'] = False
system_params['constraints'] = None
if self.mol.integrator is not None:
if self.mol.integrator.params.get('constrain_water', False):
system_params['rigidWater'] = True
if self.mol.integrator.params.get('constrain_hbonds', False):
system_params['constraints'] = opm.app.HBonds
return system_params
def get_openmm_integrator(self):
from simtk import openmm
integrator = openmm.VerletIntegrator(pint2simtk(self.params.timestep))
return integrator
def _set_openmm_state(self): # TODO: periodic state
self.sim.context.setPositions(opm.pint2simtk(self.mol.positions))
self.sim.context.setVelocities(opm.pint2simtk(self.mol.velocities))
self.sim.context.setTime(opm.pint2simtk(self.mol.time))
def to_simtk(self):
""" Return a SimTK quantity object
"""
from moldesign.interfaces.openmm import pint2simtk
return pint2simtk(self)
def to_simtk(self):
""" Return a SimTK quantity object
"""
from moldesign.interfaces.openmm import pint2simtk
return pint2simtk(self)
def get_openmm_integrator(self):
integrator = mm.LangevinIntegrator(
pint2simtk(self.params.temperature),
pint2simtk(self.params.collision_rate),
pint2simtk(self.params.timestep))
return integrator
def get_openmm_integrator(self):
integrator = mm.VerletIntegrator(pint2simtk(self.params.timestep))
return integrator
def to_simtk(self):
from moldesign.interfaces.openmm import pint2simtk
return pint2simtk(self)