AmoebaGeneralizedKirkwoodForce¶
-
class
OpenMM
::
AmoebaGeneralizedKirkwoodForce
¶ This class implements an implicit solvation force using the generalized Kirkwood/Grycuk model.
To use this class, create an
AmoebaGeneralizedKirkwoodForce
object, then calladdParticle()
once for each particle in theSystem
to define its parameters. The number of particles for which you define parameters must be equal to the number of particles in theSystem
, or else an exception will be thrown when you try to create aContext
. After a particle has been added, you can modify its force field parameters by callingsetParticleParameters()
. This will have no effect on Contexts that already exist unless you callupdateParametersInContext()
.Methods
Get the number of particles in the system.
Add the parameters for a particle.
Get the force field parameters for a particle.
Set the force field parameters for a particle.
Get the dielectric constant for the solvent.
Set the dielectric constant for the solvent.
Get the dielectric constant for the solute.
Set the dielectric constant for the solute.
Get the flag signaling whether the cavity term should be included
Set the flag signaling whether the cavity term should be included
Get the probe radius (nm) used in SASA contribution
Set the probe radius (nm) used in SASA contribution
Get the surface area factor kJ/(nm*nm) used in SASA contribution
Set the surface area factor kJ/(nm*nm) used in SASA contribution
Update the per-particle parameters in a
Context
to match those stored in thisForce
object.Returns whether or not this force makes use of periodic boundary conditions.
-
AmoebaGeneralizedKirkwoodForce
()¶
-
int
getNumParticles
() const¶ Get the number of particles in the system.
-
int
addParticle
(double charge, double radius, double scalingFactor)¶ 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.- Parameters
charge – the charge of the particle, measured in units of the proton charge
radius – the atomic radius of the particle, measured in nm
scalingFactor – the scaling factor for the particle
- Returns
the index of the particle that was added
-
void
getParticleParameters
(int index, double &charge, double &radius, double &scalingFactor) const¶ Get the force field parameters for a particle.
- Parameters
index – the index of the particle for which to get parameters
charge – [out] the charge of the particle, measured in units of the proton charge
radius – [out] the atomic radius of the particle, measured in nm
scalingFactor – [out] the scaling factor for the particle
-
void
setParticleParameters
(int index, double charge, double radius, double scalingFactor)¶ Set the force field parameters for a particle.
- Parameters
index – the index of the particle for which to set parameters
charge – the charge of the particle, measured in units of the proton charge
radius – the atomic radius of the particle, measured in nm
scalingFactor – the scaling factor for the particle
-
double
getSolventDielectric
() const¶ Get the dielectric constant for the solvent.
-
void
setSolventDielectric
(double dielectric)¶ Set the dielectric constant for the solvent.
-
double
getSoluteDielectric
() const¶ Get the dielectric constant for the solute.
-
void
setSoluteDielectric
(double dielectric)¶ Set the dielectric constant for the solute.
-
int
getIncludeCavityTerm
() const¶ Get the flag signaling whether the cavity term should be included
-
void
setIncludeCavityTerm
(int includeCavityTerm)¶ Set the flag signaling whether the cavity term should be included
-
double
getProbeRadius
() const¶ Get the probe radius (nm) used in SASA contribution
-
void
setProbeRadius
(double probeRadius)¶ Set the probe radius (nm) used in SASA contribution
-
double
getSurfaceAreaFactor
() const¶ Get the surface area factor kJ/(nm*nm) used in SASA contribution
-
void
setSurfaceAreaFactor
(double surfaceAreaFactor)¶ Set the surface area factor kJ/(nm*nm) used in SASA contribution
-
void
updateParametersInContext
(Context &context)¶ Update the per-particle parameters in a
Context
to match those stored in thisForce
object. This method provides an efficient method to update certain parameters in an existingContext
without needing to reinitialize it. Simply callsetParticleParameters()
to modify this object’s parameters, then callupdateParametersInContext()
to copy them over to theContext
.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 theContext
.
-
bool
usesPeriodicBoundaryConditions
() const¶ Returns whether or not this force makes use of periodic boundary conditions.
- Returns
true if nonbondedMethod uses PBC and false otherwise
-