def __init__(self,
temperature,
nbins,
store_filename,
protocol=None,
mm=None):
"""
Initialize a Hamiltonian exchange simulation object.
ARGUMENTS
store_filename (string) - name of NetCDF file to bind to for simulation output and checkpointing
OPTIONAL ARGUMENTS
protocol (dict) - Optional protocol to use for specifying simulation protocol as a dict. Provided keywords will be matched to object variables to replace defaults.
NOTES
von Mises distribution used for restraints
http://en.wikipedia.org/wiki/Von_Mises_distribution
"""
import simtk.pyopenmm.extras.testsystems as testsystems
# Create reference system and state.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
self.reference_system = system
self.reference_state = repex.ThermodynamicState(
system=system, temperature=temperature)
self.nbins = nbins
self.kT = (repex.kB * temperature)
self.beta = 1.0 / self.kT
self.delta = 360.0 / float(
nbins) * units.degrees # bin spacing (angular)
self.sigma = self.delta / 3.0 # standard deviation (angular)
self.kappa = (self.sigma / units.radians)**(
-2) # kappa parameter (unitless)
# Create list of thermodynamic states with different bias potentials.
states = list()
# Create a state without a biasing potential.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
state = repex.ThermodynamicState(system=system,
temperature=temperature)
states.append(state)
# Create states with biasing potentials.
for phi_index in range(nbins):
for psi_index in range(nbins):
print "bin (%d,%d)" % (phi_index, psi_index)
# Create system.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
# Add biasing potentials.
phi0 = (float(phi_index) +
0.5) * self.delta - 180.0 * units.degrees
psi0 = (float(psi_index) +
0.5) * self.delta - 180.0 * units.degrees
force = openmm.CustomTorsionForce(
'-kT * kappa * cos(theta - theta0)')
force.addGlobalParameter('kT',
self.kT / units.kilojoules_per_mole)
force.addPerTorsionParameter('kappa')
force.addPerTorsionParameter('theta0')
force.addTorsion(4, 6, 8, 14,
[self.kappa, phi0 / units.radians])
force.addTorsion(6, 8, 14, 16,
[self.kappa, psi0 / units.radians])
system.addForce(force)
# Add state.
state = repex.ThermodynamicState(system=system,
temperature=temperature)
states.append(state)
# Initialize replica-exchange simlulation.
ReplicaExchange.__init__(self,
states,
coordinates,
store_filename,
protocol=protocol,
mm=mm)
# Override title.
self.title = '2D umbrella sampling replica-exchange simulation created on %s' % time.asctime(
time.localtime())
return
def __init__(self, temperature, nbins, store_filename, protocol=None, mm=None):
"""
Initialize a Hamiltonian exchange simulation object.
ARGUMENTS
store_filename (string) - name of NetCDF file to bind to for simulation output and checkpointing
OPTIONAL ARGUMENTS
protocol (dict) - Optional protocol to use for specifying simulation protocol as a dict. Provided keywords will be matched to object variables to replace defaults.
NOTES
von Mises distribution used for restraints
http://en.wikipedia.org/wiki/Von_Mises_distribution
"""
import simtk.pyopenmm.extras.testsystems as testsystems
# Create reference system and state.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
self.reference_system = system
self.reference_state = repex.ThermodynamicState(system=system, temperature=temperature)
self.nbins = nbins
self.kT = (repex.kB * temperature)
self.beta = 1.0 / self.kT
self.delta = 360.0 / float(nbins) * units.degrees # bin spacing (angular)
self.sigma = self.delta/3.0 # standard deviation (angular)
self.kappa = (self.sigma / units.radians)**(-2) # kappa parameter (unitless)
# Create list of thermodynamic states with different bias potentials.
states = list()
# Create a state without a biasing potential.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
state = repex.ThermodynamicState(system=system, temperature=temperature)
states.append(state)
# Create states with biasing potentials.
for phi_index in range(nbins):
for psi_index in range(nbins):
print "bin (%d,%d)" % (phi_index, psi_index)
# Create system.
[system, coordinates] = testsystems.AlanineDipeptideImplicit()
# Add biasing potentials.
phi0 = (float(phi_index) + 0.5) * self.delta - 180.0 * units.degrees
psi0 = (float(psi_index) + 0.5) * self.delta - 180.0 * units.degrees
force = openmm.CustomTorsionForce('-kT * kappa * cos(theta - theta0)')
force.addGlobalParameter('kT', self.kT / units.kilojoules_per_mole)
force.addPerTorsionParameter('kappa')
force.addPerTorsionParameter('theta0')
force.addTorsion(4, 6, 8, 14, [self.kappa, phi0 / units.radians])
force.addTorsion(6, 8, 14, 16, [self.kappa, psi0 / units.radians])
system.addForce(force)
# Add state.
state = repex.ThermodynamicState(system=system, temperature=temperature)
states.append(state)
# Initialize replica-exchange simlulation.
ReplicaExchange.__init__(self, states, coordinates, store_filename, protocol=protocol, mm=mm)
# Override title.
self.title = '2D umbrella sampling replica-exchange simulation created on %s' % time.asctime(time.localtime())
return
