AmoebaGeneralizedKirkwoodForce

class openmm.openmm.AmoebaGeneralizedKirkwoodForce(*args)

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

__init__(self) → AmoebaGeneralizedKirkwoodForce

__init__(self, other) → AmoebaGeneralizedKirkwoodForce

This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.

To use this class, create an AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in the System, or else an exception will be thrown when you try to create a Context. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

Methods

__init__(-> AmoebaGeneralizedKirkwoodForce)	This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.
addParticle(-> int)	Add the parameters for a particle.
getDescreenOffset(self)	Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.
getDielectricOffset(self)	Get the dielectric offset (nm) used for cavity contribution.
getForceGroup(self)	Get the force group this Force belongs to.
getIncludeCavityTerm(self)	Get the flag signaling whether the cavity term should be included
getName(self)	Get the name of this Force.
getNumParticles(self)	Get the number of particles in the system.
getParticleParameters(self, index)	Get the force field parameters for a particle.
getProbeRadius(self)	Get the probe radius (nm) used for the cavity contribution.
getSoluteDielectric(self)	Get the dielectric constant for the solute.
getSolventDielectric(self)	Get the dielectric constant for the solvent.
getSurfaceAreaFactor(self)	Get the surface area factor kJ/(nm*nm) used in SASA contribution
getTanhParameters(self)	Get Tanh function parameters b0, b1 and b2.
getTanhRescaling(self)	Get the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces.
setDescreenOffset(self, descreenOffet)	Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.
setDielectricOffset(self, dielectricOffset)	Set the dielectric offset (nm) used for cavity contribution.
setForceGroup(self, group)	Set the force group this Force belongs to.
setIncludeCavityTerm(self, includeCavityTerm)	Set the flag signaling whether the cavity term should be included.
setName(self, name)	Set the name of this Force.
setParticleParameters(self, index, charge, …)	Set the force field parameters for a particle.
setProbeRadius(self, probeRadius)	Set the probe radius (nm) used for the cavity contribution.
setSoluteDielectric(self, dielectric)	Set the dielectric constant for the solute.
setSolventDielectric(self, dielectric)	Set the dielectric constant for the solvent.
setSurfaceAreaFactor(self, surfaceAreaFactor)	Set the surface area factor kJ/(nm*nm) used in SASA contribution.
setTanhParameters(self, b0, b1, b2)	Set the the Tanh function parameters to account for interstitial spaces.
setTanhRescaling(self, tanhRescale)	Set the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces.
updateParametersInContext(self, context)	Update the per-particle 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

thisown

The membership flag

property thisown

The membership flag

getNumParticles(self) → int

Get the number of particles in the system.

addParticle(self, charge, radius, scalingFactor) → int

addParticle(self, charge, radius, scalingFactor, descreenRadius, neckFactor) → int

Add the parameters for a particle. This should be called once for each particle in the System. When it is called for the i’th time, it specifies the parameters for the i’th particle.

For generalized Born / generalized Kirkwood methods, the radius of each atom has two roles. The first is to define the base radius of the atom when computing its effective radius. This base radius is usually parameterized against solvation free energy differences. The second role is to describe how much continuum water is displaced when the atom descreens water for the calculation of the Born radii of other atoms. Separation of the two roles into the “radius” and “descreenRadius” parameters gives model developers more control over these separate roles.

For example, the fitting of base “radius” values will usually result in deviation from the force field’s van der Waals definition of Rmin (or sigma). The descreenRadius can be defined separately using force field van der Waals Rmin values, which maintains consistency of atomic sizes during the HCT pairwise descreening integral. The “scalingFactor” is applied to the descreenRadius during the HCT pairwise descreening integral, while the neckFactor (if greater than zero) includes neck contributions to descreening.

Parameters

• charge (double) – the charge of the particle, measured in units of the proton charge

• radius (double) – the atomic radius of the particle, measured in nm

• scalingFactor (double) – the scaling factor for the particle (unitless)

• descreenRadius (double) – the atomic radius of the particle for descreening, measure in nm

• neckFactor (double) – the scaling factor for interstitial neck descreening (unitless)

Returns

the index of the particle that was added

Return type

int

getParticleParameters(self, index)

Get the force field parameters for a particle.

Parameters

index (int) – the index of the particle for which to get parameters

Returns

• charge (double) – the charge of the particle, measured in units of the proton charge

• radius (double) – the atomic radius of the particle, measured in nm

• scalingFactor (double) – the scaling factor for the particle

• descreenRadius (double) – the atomic radius of the particle for descreening, measure in nm

• neckFactor (double) – the scaling factor for interstitial neck descreening (unitless)

setParticleParameters(self, index, charge, radius, scalingFactor, descreenRadius, neckFactor)

Set the force field parameters for a particle.

Parameters

• index (int) – the index of the particle for which to set parameters

• charge (double) – the charge of the particle, measured in units of the proton charge

• radius (double) – the atomic radius of the particle, measured in nm

• scalingFactor (double) – the scaling factor for the particle

• descreenRadius (double) – the atomic radius of the particle for descreening, measure in nm

• neckFactor (double) – the scaling factor for interstitial neck descreening (unitless)

getSolventDielectric(self) → double

Get the dielectric constant for the solvent.

setSolventDielectric(self, dielectric)

Set the dielectric constant for the solvent.

getSoluteDielectric(self) → double

Get the dielectric constant for the solute.

setSoluteDielectric(self, dielectric)

Set the dielectric constant for the solute.

Parameters

dielectric (double) – The solute dielectric constant.

getTanhRescaling(self) → bool

Get the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces. If True then tanh rescaling is used.

setTanhRescaling(self, tanhRescale)

Set the flag signaling whether the solute descreening integral is rescaled by a Tanh function to account for interstitial spaces.

Parameters

tanhRescale (bool) – False to turn off Tanh rescaling; true to turn on.

getTanhParameters(self)

Get Tanh function parameters b0, b1 and b2.

Parameters

• b0 (double) – The first tanh parameter.

• b1 (double) – The second tanh parameter.

• b2 (double) – The third tanh parameter.

setTanhParameters(self, b0, b1, b2)

Set the the Tanh function parameters to account for interstitial spaces.

Parameters

• b0 (double) – The first tanh parameter.

• b1 (double) – The second tanh parameter.

• b2 (double) – The third tanh parameter.

getDescreenOffset(self) → double

Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.

setDescreenOffset(self, descreenOffet)

Get the offset added to the atomic radius of each atom that sets the beginning of the descreening integral when calculating effective Born radii.

Parameters

descreenOffet (double) – The descreening offset (nm).

getIncludeCavityTerm(self) → int

Get the flag signaling whether the cavity term should be included

setIncludeCavityTerm(self, includeCavityTerm)

Set the flag signaling whether the cavity term should be included.

Parameters

includeCavityTerm (int) – Zero to turn off the cavity term; one to turn on.

getProbeRadius(self) → double

Get the probe radius (nm) used for the cavity contribution.

setProbeRadius(self, probeRadius)

Set the probe radius (nm) used for the cavity contribution.

Parameters

probeRadius (double) – The probeRadius for the cavity term.

getDielectricOffset(self) → double

Get the dielectric offset (nm) used for cavity contribution.

setDielectricOffset(self, dielectricOffset)

Set the dielectric offset (nm) used for cavity contribution.

Parameters

dielectricOffset (double) – The dielectric offset (nm).

getSurfaceAreaFactor(self) → double

Get the surface area factor kJ/(nm*nm) used in SASA contribution

setSurfaceAreaFactor(self, surfaceAreaFactor)

Set the surface area factor kJ/(nm*nm) used in SASA contribution.

Parameters

surfaceAreaFactor (double) – The surface area factor in kJ/(nm*nm).

updateParametersInContext(self, context)

Update the per-particle 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 setParticleParameters() to modify this object’s parameters, then call updateParametersInContext() to copy them over to the Context.

The only information this method updates is the values of per-particle parameters. All other aspects of the Force (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.

usesPeriodicBoundaryConditions(self) → bool

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

Returns

true if nonbondedMethod uses PBC and false otherwise

Return type

bool

getForceGroup(self) → int

Get the force group this Force belongs to.

getName(self) → std::string const &

Get the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.

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).

setName(self, name)

Set the name of this Force. This is an arbitrary, user modifiable identifier. By default it equals the class name, but you can change it to anything useful.