# openmmtools.forces.FlatBottomRestraintBondForce¶

class openmmtools.forces.FlatBottomRestraintBondForce(spring_constant, well_radius, *args, **kwargs)[source]

A restraint between two atoms using a flat potential well with harmonic walls.

This is a version of FlatBottomRestraintForce that can be used with OpenCL 32-bit platforms. It supports atom groups with only a single atom.

Parameters: spring_constant : simtk.unit.Quantity The spring constant K (see energy expression above) in units compatible with joule/nanometer**2/mole. well_radius : simtk.unit.Quantity The distance r0 (see energy expression above) at which the harmonic restraint is imposed in units of distance. restrained_atom_index1 : int The index of the first group of atoms to restrain. restrained_atom_index2 : int The index of the second group of atoms to restrain. controlling_parameter_name : str, optional The name of the global parameter controlling the energy function. The default value is ‘lambda_restraints’. spring_constant unit.simtk.Quantity: The spring constant K (units of energy/mole/length^2). well_radius unit.simtk.Quantity: The distance at which the harmonic restraint is imposed (units of length). restrained_atom_indices1 The indices of the first group of restrained atoms. restrained_atom_indices2 The indices of the first group of restrained atoms. restraint_parameters OrderedDict: The restraint parameters in dictionary form. controlling_parameter_name str: The name of the global parameter controlling the energy function (read-only).

Methods

 addBond(self, particle1, particle2, parameters) addBond(self, particle1, particle2) -> int addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter. addGlobalParameter(self, name, defaultValue) Add a new global parameter that the interaction may depend on. addPerBondParameter(self, name) Add a new per-bond parameter that the interaction may depend on. compute_standard_state_correction(…[, …]) Return the standard state correction of the restraint. deserialize_xml(xml_serialization) Shortcut to deserialize the XML representation and the restore interface. distance_at_energy(potential_energy) Compute the distance at which the potential energy is potential_energy. getBondParameters(self, index) Get the force field parameters for a bond term. getEnergyFunction(self) Get the algebraic expression that gives the interaction energy for each bond getEnergyParameterDerivativeName(self, index) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy. getForceGroup(self) Get the force group this Force belongs to. getGlobalParameterDefaultValue(self, index) Get the default value of a global parameter. getGlobalParameterName(self, index) Get the name of a global parameter. getNumBonds(self) Get the number of bonds for which force field parameters have been defined. getNumEnergyParameterDerivatives(self) Get the number of global parameters with respect to which the derivative of the energy should be computed. getNumGlobalParameters(self) Get the number of global parameters that the interaction depends on. getNumPerBondParameters(self) Get the number of per-bond parameters that the interaction depends on. getPerBondParameterName(self, index) Get the name of a per-bond parameter. is_restorable(openmm_object) Check if the custom integrator or force has a restorable interface. restore_interface(openmm_object) Restore the original interface of an OpenMM custom force or integrator. setBondParameters(self, index, particle1, …) Set the force field parameters for a bond term. setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each bond setForceGroup(self, group) Set the force group this Force belongs to. setGlobalParameterDefaultValue(self, index, …) Set the default value of a global parameter. setGlobalParameterName(self, index, name) Set the name of a global parameter. setPerBondParameterName(self, index, name) Set the name of a per-bond parameter. setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements. updateParametersInContext(self, context) Update the per-bond parameters in a Context to match those stored in this Force object. usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.
__init__(spring_constant, well_radius, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

Methods

 __init__(spring_constant, well_radius, …) Initialize self. addBond(self, particle1, particle2, parameters) addBond(self, particle1, particle2) -> int addEnergyParameterDerivative(self, name) Request that this Force compute the derivative of its energy with respect to a global parameter. addGlobalParameter(self, name, defaultValue) Add a new global parameter that the interaction may depend on. addPerBondParameter(self, name) Add a new per-bond parameter that the interaction may depend on. compute_standard_state_correction(…[, …]) Return the standard state correction of the restraint. deserialize_xml(xml_serialization) Shortcut to deserialize the XML representation and the restore interface. distance_at_energy(potential_energy) Compute the distance at which the potential energy is potential_energy. getBondParameters(self, index) Get the force field parameters for a bond term. getEnergyFunction(self) Get the algebraic expression that gives the interaction energy for each bond getEnergyParameterDerivativeName(self, index) Get the name of a global parameter with respect to which this Force should compute the derivative of the energy. getForceGroup(self) Get the force group this Force belongs to. getGlobalParameterDefaultValue(self, index) Get the default value of a global parameter. getGlobalParameterName(self, index) Get the name of a global parameter. getNumBonds(self) Get the number of bonds for which force field parameters have been defined. getNumEnergyParameterDerivatives(self) Get the number of global parameters with respect to which the derivative of the energy should be computed. getNumGlobalParameters(self) Get the number of global parameters that the interaction depends on. getNumPerBondParameters(self) Get the number of per-bond parameters that the interaction depends on. getPerBondParameterName(self, index) Get the name of a per-bond parameter. is_restorable(openmm_object) Check if the custom integrator or force has a restorable interface. restore_interface(openmm_object) Restore the original interface of an OpenMM custom force or integrator. setBondParameters(self, index, particle1, …) Set the force field parameters for a bond term. setEnergyFunction(self, energy) Set the algebraic expression that gives the interaction energy for each bond setForceGroup(self, group) Set the force group this Force belongs to. setGlobalParameterDefaultValue(self, index, …) Set the default value of a global parameter. setGlobalParameterName(self, index, name) Set the name of a global parameter. setPerBondParameterName(self, index, name) Set the name of a per-bond parameter. setUsesPeriodicBoundaryConditions(self, periodic) Set whether this force should apply periodic boundary conditions when calculating displacements. updateParametersInContext(self, context) Update the per-bond parameters in a Context to match those stored in this Force object. usesPeriodicBoundaryConditions(self) Returns whether or not this force makes use of periodic boundary conditions.

Attributes

 controlling_parameter_name str: The name of the global parameter controlling the energy function (read-only). restrained_atom_indices1 The indices of the first group of restrained atoms. restrained_atom_indices2 The indices of the first group of restrained atoms. restraint_parameters OrderedDict: The restraint parameters in dictionary form. spring_constant unit.simtk.Quantity: The spring constant K (units of energy/mole/length^2). well_radius unit.simtk.Quantity: The distance at which the harmonic restraint is imposed (units of length).
addBond(self, particle1, particle2, parameters) → int

Add a bond term to the force field.

Parameters: particle1 : int the index of the first particle connected by the bond particle2 : int the index of the second particle connected by the bond parameters : vector< double > the list of parameters for the new bond int the index of the bond that was added
addEnergyParameterDerivative(self, name)

Request that this Force compute the derivative of its energy with respect to a global parameter. The parameter must have already been added with addGlobalParameter().

Parameters: name : string the name of the parameter
addGlobalParameter(self, name, defaultValue) → int

Add a new global parameter that the interaction may depend on. The default value provided to this method is the initial value of the parameter in newly created Contexts. You can change the value at any time by calling setParameter() on the Context.

Parameters: name : string the name of the parameter defaultValue : double the default value of the parameter int the index of the parameter that was added
addPerBondParameter(self, name) → int

Add a new per-bond parameter that the interaction may depend on.

Parameters: name : string the name of the parameter int the index of the parameter that was added
compute_standard_state_correction(thermodynamic_state, square_well=False, radius_cutoff=None, energy_cutoff=None, max_volume=None)

Return the standard state correction of the restraint.

The standard state correction is computed as

• log(V_standard / V_restraint)

where V_standard is the volume at standard state concentration and V_restraint is the restraint volume. V_restraint is bounded by the volume of the periodic box.

The square_well parameter, can be used to re-compute the standard state correction when removing the bias introduced by the restraint.

Parameters: thermodynamic_state : states.ThermodynamicState The thermodynamic state at which to compute the standard state correction. square_well : bool, optional If True, this computes the standard state correction assuming the restraint to obey a square well potential. The energy cutoff is still applied to the original energy potential. radius_cutoff : simtk.unit.Quantity, optional The maximum distance achievable by the restraint (units compatible with nanometers). This is equivalent to placing a hard wall potential at this distance. energy_cutoff : float, optional The maximum potential energy achievable by the restraint in kT. This is equivalent to placing a hard wall potential at a distance such that potential_energy(distance) == energy_cutoff. max_volume : simtk.unit.Quantity or ‘system’, optional The volume of the periodic box (units compatible with nanometer**3). This must be provided the thermodynamic state is in NPT. If the string ‘system’ is passed, the maximum volume is computed from the system box vectors (this has no effect if the system is not periodic). correction : float The unit-less standard state correction in kT at the given thermodynamic state. TypeError If the thermodynamic state is in the NPT ensemble, and max_volume is not provided, or if the system is non-periodic and no cutoff is given.
controlling_parameter_name

str: The name of the global parameter controlling the energy function (read-only).

classmethod deserialize_xml(xml_serialization)

Shortcut to deserialize the XML representation and the restore interface.

Parameters: xml_serialization : str The XML representation of the OpenMM custom force/integrator. openmm_object The deserialized OpenMM force/integrator with the original interface restored (if restorable).
distance_at_energy(potential_energy)

Compute the distance at which the potential energy is potential_energy.

Parameters: potential_energy : simtk.unit.Quantity The potential energy of the restraint (units of energy/mole). distance : simtk.unit.Quantity The distance at which the potential energy is potential_energy (units of length).
getBondParameters(self, index)

Get the force field parameters for a bond term.

Parameters: index : int the index of the bond for which to get parameters particle1 : int the index of the first particle connected by the bond particle2 : int the index of the second particle connected by the bond parameters : vector< double > the list of parameters for the bond
getEnergyFunction(self) → std::string const &

Get the algebraic expression that gives the interaction energy for each bond

getEnergyParameterDerivativeName(self, index) → std::string const &

Get the name of a global parameter with respect to which this Force should compute the derivative of the energy.

Parameters: index : int the index of the parameter derivative, between 0 and getNumEnergyParameterDerivatives() string the parameter name
getForceGroup(self) → int

Get the force group this Force belongs to.

getGlobalParameterDefaultValue(self, index) → double

Get the default value of a global parameter.

Parameters: index : int the index of the parameter for which to get the default value double the parameter default value
getGlobalParameterName(self, index) → std::string const &

Get the name of a global parameter.

Parameters: index : int the index of the parameter for which to get the name string the parameter name
getNumBonds(self) → int

Get the number of bonds for which force field parameters have been defined.

getNumEnergyParameterDerivatives(self) → int

Get the number of global parameters with respect to which the derivative of the energy should be computed.

getNumGlobalParameters(self) → int

Get the number of global parameters that the interaction depends on.

getNumPerBondParameters(self) → int

Get the number of per-bond parameters that the interaction depends on.

getPerBondParameterName(self, index) → std::string const &

Get the name of a per-bond parameter.

Parameters: index : int the index of the parameter for which to get the name string the parameter name
classmethod is_restorable(openmm_object)

Check if the custom integrator or force has a restorable interface.

Parameters: openmm_object : object The custom integrator or force to check. True if the object has a restorable interface, False otherwise.
classmethod restore_interface(openmm_object)

Restore the original interface of an OpenMM custom force or integrator.

The function restore the methods of the original class that inherited from RestorableOpenMMObject. Return False if the interface could not be restored.

Parameters: openmm_object : object The object to restore. True if the original class interface could be restored, False otherwise.
restrained_atom_indices1

The indices of the first group of restrained atoms.

restrained_atom_indices2

The indices of the first group of restrained atoms.

restraint_parameters

OrderedDict: The restraint parameters in dictionary form.

setBondParameters(self, index, particle1, particle2, parameters) setBondParameters(self, index, particle1, particle2)

Set the force field parameters for a bond term.

Parameters: index : int the index of the bond for which to set parameters particle1 : int the index of the first particle connected by the bond particle2 : int the index of the second particle connected by the bond parameters : vector< double > the list of parameters for the bond
setEnergyFunction(self, energy)

Set the algebraic expression that gives the interaction energy for each bond

setForceGroup(self, group)

Set the force group this Force belongs to.

Parameters: group : int the group index. Legal values are between 0 and 31 (inclusive).
setGlobalParameterDefaultValue(self, index, defaultValue)

Set the default value of a global parameter.

Parameters: index : int the index of the parameter for which to set the default value defaultValue : double the default value of the parameter
setGlobalParameterName(self, index, name)

Set the name of a global parameter.

Parameters: index : int the index of the parameter for which to set the name name : string the name of the parameter
setPerBondParameterName(self, index, name)

Set the name of a per-bond parameter.

Parameters: index : int the index of the parameter for which to set the name name : string the name of the parameter
setUsesPeriodicBoundaryConditions(self, periodic)

Set whether this force should apply periodic boundary conditions when calculating displacements. Usually this is not appropriate for bonded forces, but there are situations when it can be useful.

spring_constant

unit.simtk.Quantity: The spring constant K (units of energy/mole/length^2).

updateParametersInContext(self, context)

Update the per-bond parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setBondParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

This method has several limitations. The only information it updates is the values of per-bond parameters. All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing the Context. The set of particles involved in a bond cannot be changed, nor can new bonds be added.

usesPeriodicBoundaryConditions(self) → bool

Returns whether or not this force makes use of periodic boundary conditions.

Returns: bool true if force uses PBC and false otherwise
well_radius

unit.simtk.Quantity: The distance at which the harmonic restraint is imposed (units of length).