def create(self,
reference_state,
alchemical_states,
positions,
displacement_sigma=None,
mc_atoms=None,
options=None,
metadata=None):
"""
Initialize a modified Hamiltonian exchange simulation object.
Parameters
----------
reference_state : ThermodynamicState
reference state containing all thermodynamic parameters and reference System object'
alchemical_states : list of AlchemicalState
list of alchemical states (one per replica)
positions : simtk.unit.Quantity of numpy natoms x 3 with units length
positions (or a list of positions objects) for initial assignment of replicas (will be used in round-robin assignment)
displacement_sigma : simtk.unit.Quantity with units distance
size of displacement trial for Monte Carlo displacements, if specified (default: 1 nm)
ligand_atoms : list of int, optional, default=None
atoms to use for trial displacements for translational and orientational Monte Carlo trials, if specified (all atoms if None)
options : dict, optional, default=None
Optional dict to use for specifying simulation options. Provided keywords will be matched to object variables to replace defaults.
metadata : dict, optional, default=None
metadata to store in a 'metadata' group in store file
"""
# If an empty set is specified for mc_atoms, set this to None.
if mc_atoms is not None:
if len(mc_atoms) == 0:
mc_atoms = None
# Store trial displacement magnitude and atoms to rotate in MC move.
self.displacement_sigma = 1.0 * unit.nanometer
if mc_atoms is not None:
self.mc_atoms = np.array(mc_atoms)
self.mc_displacement = True
self.mc_rotation = True
else:
self.mc_atoms = None
self.mc_displacement = False
self.mc_rotation = False
self.displacement_trials_accepted = 0 # number of MC displacement trials accepted
self.rotation_trials_accepted = 0 # number of MC displacement trials accepted
# Store reference system.
self.reference_system = copy.deepcopy(reference_state.system)
# TODO: Form metadata dict.
# Initialize replica-exchange simlulation.
states = list()
for alchemical_state in alchemical_states:
state = ThermodynamicState(system=self.reference_system,
temperature=reference_state.temperature,
pressure=reference_state.pressure)
setattr(state, 'alchemical_state',
copy.deepcopy(alchemical_state)) # attach alchemical state
states.append(state)
# Initialize replica-exchange simlulation.
ReplicaExchange.create(self,
states,
positions,
options=options,
metadata=metadata)
# Override title.
self.title = 'Alchemical Hamiltonian exchange simulation created using HamiltonianExchange class of repex.py on %s' % time.asctime(
time.localtime())
return
def create(self, reference_state, alchemical_states, positions, displacement_sigma=None, mc_atoms=None, options=None, metadata=None):
"""
Initialize a modified Hamiltonian exchange simulation object.
Parameters
----------
reference_state : ThermodynamicState
reference state containing all thermodynamic parameters and reference System object'
alchemical_states : list of AlchemicalState
list of alchemical states (one per replica)
positions : simtk.unit.Quantity of numpy natoms x 3 with units length
positions (or a list of positions objects) for initial assignment of replicas (will be used in round-robin assignment)
displacement_sigma : simtk.unit.Quantity with units distance
size of displacement trial for Monte Carlo displacements, if specified (default: 1 nm)
ligand_atoms : list of int, optional, default=None
atoms to use for trial displacements for translational and orientational Monte Carlo trials, if specified (all atoms if None)
options : dict, optional, default=None
Optional dict to use for specifying simulation options. Provided keywords will be matched to object variables to replace defaults.
metadata : dict, optional, default=None
metadata to store in a 'metadata' group in store file
"""
# If an empty set is specified for mc_atoms, set this to None.
if mc_atoms is not None:
if len(mc_atoms) == 0:
mc_atoms = None
# Store trial displacement magnitude and atoms to rotate in MC move.
self.displacement_sigma = 1.0 * unit.nanometer
if mc_atoms is not None:
self.mc_atoms = np.array(mc_atoms)
self.mc_displacement = True
self.mc_rotation = True
else:
self.mc_atoms = None
self.mc_displacement = False
self.mc_rotation = False
self.displacement_trials_accepted = 0 # number of MC displacement trials accepted
self.rotation_trials_accepted = 0 # number of MC displacement trials accepted
# Store reference system.
self.reference_system = copy.deepcopy(reference_state.system)
# TODO: Form metadata dict.
# Initialize replica-exchange simlulation.
states = list()
for alchemical_state in alchemical_states:
state = ThermodynamicState(system=self.reference_system, temperature=reference_state.temperature, pressure=reference_state.pressure)
setattr(state, 'alchemical_state', copy.deepcopy(alchemical_state)) # attach alchemical state
states.append(state)
# Initialize replica-exchange simlulation.
ReplicaExchange.create(self, states, positions, options=options, metadata=metadata)
# Override title.
self.title = 'Alchemical Hamiltonian exchange simulation created using HamiltonianExchange class of repex.py on %s' % time.asctime(time.localtime())
return
