openmmtools.forces.UnshiftedReactionFieldForce

class openmmtools.forces.UnshiftedReactionFieldForce(cutoff_distance=Quantity(value=15, unit=angstrom), switch_width=Quantity(value=1.0, unit=angstrom), reaction_field_dielectric=78.3)[source]

A force modelling switched reaction-field electrostatics.

Contrarily to a normal NonbondedForce with CutoffPeriodic nonbonded method, this force sets the c_rf to 0.0 and uses a switching function to avoid forces discontinuities at the cutoff distance.

Parameters:
cutoff_distanceopenmm.unit.Quantity, default 15*angstroms

The cutoff distance (units of distance).

switch_widthopenmm.unit.Quantity, default 1.0*angstrom

Switch width for electrostatics (units of distance).

reaction_field_dielectricfloat

The dielectric constant used for the solvent.

Attributes:
thisown

The membership flag

Methods

addComputedValue(self, name, expression)

Add a computed value to calculate for each particle.

addEnergyParameterDerivative(self, name)

Request that this Force compute the derivative of its energy with respect to a global parameter.

addExclusion(self, particle1, particle2)

Add a particle pair to the list of interactions that should be excluded.

addFunction(self, name, values, min, max)

Add a tabulated function that may appear in the energy expression.

addGlobalParameter(self, name, defaultValue)

Add a new global parameter that the interaction may depend on.

addInteractionGroup(self, set1, set2)

Add an interaction group.

addParticle(self[, parameters])

Add the nonbonded force parameters for a particle.

addPerParticleParameter(self, name)

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

addTabulatedFunction(self, name, function)

Add a tabulated function that may appear in the energy expression.

createExclusionsFromBonds(self, bonds, ...)

Identify exclusions based on the molecular topology.

from_nonbonded_force(nonbonded_force[, ...])

Copy constructor from an OpenMM NonbondedForce.

from_system(system[, switch_width])

Copy constructor from the first OpenMM NonbondedForce in system.

getComputedValueParameters(self, index)

Get the properties of a computed value.

getCutoffDistance(self)

Get the cutoff distance (in nm) being used for nonbonded interactions.

getEnergyFunction(self)

Get the algebraic expression that gives the interaction energy between two particles

getEnergyParameterDerivativeName(self, index)

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

getExclusionParticles(self, index)

Get the particles in a pair whose interaction should be excluded.

getForceGroup(self)

Get the force group this Force belongs to.

getFunctionParameters(self, index)

Get the parameters for a tabulated function that may appear in the energy expression.

getGlobalParameterDefaultValue(self, index)

Get the default value of a global parameter.

getGlobalParameterName(self, index)

Get the name of a global parameter.

getInteractionGroupParameters(self, index)

Get the parameters for an interaction group.

getName(self)

Get the name of this Force.

getNonbondedMethod(self)

Get the method used for handling long range nonbonded interactions.

getNumComputedValues(self)

Get the number of per-particle computed values the interaction depends on.

getNumEnergyParameterDerivatives(self)

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

getNumExclusions(self)

Get the number of particle pairs whose interactions should be excluded.

getNumFunctions(self)

Get the number of tabulated functions that have been defined.

getNumGlobalParameters(self)

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

getNumInteractionGroups(self)

Get the number of interaction groups that have been defined.

getNumParticles(self)

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

getNumPerParticleParameters(self)

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

getNumTabulatedFunctions(self)

Get the number of tabulated functions that have been defined.

getParticleParameters(self, index)

Get the nonbonded force parameters for a particle.

getPerParticleParameterName(self, index)

Get the name of a per-particle parameter.

getSwitchingDistance(self)

Get the distance at which the switching function begins to reduce the interaction.

getTabulatedFunction(-> TabulatedFunction)

Get a reference to a tabulated function that may appear in the energy expression.

getTabulatedFunctionName(self, index)

Get the name of a tabulated function that may appear in the energy expression.

getUseLongRangeCorrection(self)

Get whether to add a correction to the energy to compensate for the cutoff and switching function.

getUseSwitchingFunction(self)

Get whether a switching function is applied to the interaction.

setComputedValueParameters(self, index, ...)

Set the properties of a computed value.

setCutoffDistance(self, distance)

Set the cutoff distance (in nm) being used for nonbonded interactions.

setEnergyFunction(self, energy)

Set the algebraic expression that gives the interaction energy between two particles

setExclusionParticles(self, index, ...)

Set the particles in a pair whose interaction should be excluded.

setForceGroup(self, group)

Set the force group this Force belongs to.

setFunctionParameters(self, index, name, ...)

Set the parameters for a tabulated function that may appear in the energy expression.

setGlobalParameterDefaultValue(self, index, ...)

Set the default value of a global parameter.

setGlobalParameterName(self, index, name)

Set the name of a global parameter.

setInteractionGroupParameters(self, index, ...)

Set the parameters for an interaction group.

setName(self, name)

Set the name of this Force.

setNonbondedMethod(self, method)

Set the method used for handling long range nonbonded interactions.

setParticleParameters(self, index, parameters)

Set the nonbonded force parameters for a particle.

setPerParticleParameterName(self, index, name)

Set the name of a per-particle parameter.

setSwitchingDistance(self, distance)

Set the distance at which the switching function begins to reduce the interaction.

setUseLongRangeCorrection(self, use)

Set whether to add a correction to the energy to compensate for the cutoff and switching function.

setUseSwitchingFunction(self, use)

Set whether a switching function is applied to the interaction.

updateParametersInContext(self, context)

Update the per-particle parameters and tabulated functions 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__(self, energy) CustomNonbondedForce[source]
__init__(self, rhs) CustomNonbondedForce

Create a CustomNonbondedForce.

Parameters:
energystring

an algebraic expression giving the interaction energy between two particles as a function of r, the distance between them, as well as any global and per-particle parameters

Methods

__init__(-> CustomNonbondedForce)

Create a CustomNonbondedForce.

addComputedValue(self, name, expression)

Add a computed value to calculate for each particle.

addEnergyParameterDerivative(self, name)

Request that this Force compute the derivative of its energy with respect to a global parameter.

addExclusion(self, particle1, particle2)

Add a particle pair to the list of interactions that should be excluded.

addFunction(self, name, values, min, max)

Add a tabulated function that may appear in the energy expression.

addGlobalParameter(self, name, defaultValue)

Add a new global parameter that the interaction may depend on.

addInteractionGroup(self, set1, set2)

Add an interaction group.

addParticle(self[, parameters])

Add the nonbonded force parameters for a particle.

addPerParticleParameter(self, name)

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

addTabulatedFunction(self, name, function)

Add a tabulated function that may appear in the energy expression.

createExclusionsFromBonds(self, bonds, ...)

Identify exclusions based on the molecular topology.

from_nonbonded_force(nonbonded_force[, ...])

Copy constructor from an OpenMM NonbondedForce.

from_system(system[, switch_width])

Copy constructor from the first OpenMM NonbondedForce in system.

getComputedValueParameters(self, index)

Get the properties of a computed value.

getCutoffDistance(self)

Get the cutoff distance (in nm) being used for nonbonded interactions.

getEnergyFunction(self)

Get the algebraic expression that gives the interaction energy between two particles

getEnergyParameterDerivativeName(self, index)

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

getExclusionParticles(self, index)

Get the particles in a pair whose interaction should be excluded.

getForceGroup(self)

Get the force group this Force belongs to.

getFunctionParameters(self, index)

Get the parameters for a tabulated function that may appear in the energy expression.

getGlobalParameterDefaultValue(self, index)

Get the default value of a global parameter.

getGlobalParameterName(self, index)

Get the name of a global parameter.

getInteractionGroupParameters(self, index)

Get the parameters for an interaction group.

getName(self)

Get the name of this Force.

getNonbondedMethod(self)

Get the method used for handling long range nonbonded interactions.

getNumComputedValues(self)

Get the number of per-particle computed values the interaction depends on.

getNumEnergyParameterDerivatives(self)

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

getNumExclusions(self)

Get the number of particle pairs whose interactions should be excluded.

getNumFunctions(self)

Get the number of tabulated functions that have been defined.

getNumGlobalParameters(self)

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

getNumInteractionGroups(self)

Get the number of interaction groups that have been defined.

getNumParticles(self)

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

getNumPerParticleParameters(self)

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

getNumTabulatedFunctions(self)

Get the number of tabulated functions that have been defined.

getParticleParameters(self, index)

Get the nonbonded force parameters for a particle.

getPerParticleParameterName(self, index)

Get the name of a per-particle parameter.

getSwitchingDistance(self)

Get the distance at which the switching function begins to reduce the interaction.

getTabulatedFunction(-> TabulatedFunction)

Get a reference to a tabulated function that may appear in the energy expression.

getTabulatedFunctionName(self, index)

Get the name of a tabulated function that may appear in the energy expression.

getUseLongRangeCorrection(self)

Get whether to add a correction to the energy to compensate for the cutoff and switching function.

getUseSwitchingFunction(self)

Get whether a switching function is applied to the interaction.

setComputedValueParameters(self, index, ...)

Set the properties of a computed value.

setCutoffDistance(self, distance)

Set the cutoff distance (in nm) being used for nonbonded interactions.

setEnergyFunction(self, energy)

Set the algebraic expression that gives the interaction energy between two particles

setExclusionParticles(self, index, ...)

Set the particles in a pair whose interaction should be excluded.

setForceGroup(self, group)

Set the force group this Force belongs to.

setFunctionParameters(self, index, name, ...)

Set the parameters for a tabulated function that may appear in the energy expression.

setGlobalParameterDefaultValue(self, index, ...)

Set the default value of a global parameter.

setGlobalParameterName(self, index, name)

Set the name of a global parameter.

setInteractionGroupParameters(self, index, ...)

Set the parameters for an interaction group.

setName(self, name)

Set the name of this Force.

setNonbondedMethod(self, method)

Set the method used for handling long range nonbonded interactions.

setParticleParameters(self, index, parameters)

Set the nonbonded force parameters for a particle.

setPerParticleParameterName(self, index, name)

Set the name of a per-particle parameter.

setSwitchingDistance(self, distance)

Set the distance at which the switching function begins to reduce the interaction.

setUseLongRangeCorrection(self, use)

Set whether to add a correction to the energy to compensate for the cutoff and switching function.

setUseSwitchingFunction(self, use)

Set whether a switching function is applied to the interaction.

updateParametersInContext(self, context)

Update the per-particle parameters and tabulated functions 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

CutoffNonPeriodic

CutoffPeriodic

NoCutoff

thisown

The membership flag