GBSAOBCForce¶

class OpenMM::GBSAOBCForce¶

This class implements an implicit solvation force using the GBSA-OBC model.

To use this class, create a GBSAOBCForce object, then call addParticle() once for each particle in the System to define its parameters. The number of particles for which you define GBSA parameters must be exactly 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().

When using this Force, the System should also include a NonbondedForce, and both objects must specify identical charges for all particles. Otherwise, the results will not be correct. Furthermore, if the nonbonded method is set to CutoffNonPeriodic or CutoffPeriodic, you should call setReactionFieldDielectric(1.0) on the NonbondedForce to turn off the reaction field approximation, which does not produce correct results when combined with GBSA.

Methods

`GBSAOBCForce`	Create a `GBSAOBCForce`.
`getNumParticles`	Get the number of particles in the system.
`addParticle`	Add the GBSA parameters for a particle.
`getParticleParameters`	Get the force field parameters for a particle.
`setParticleParameters`	Set the force field parameters for a particle.
`getSolventDielectric`	Get the dielectric constant for the solvent.
`setSolventDielectric`	Set the dielectric constant for the solvent.
`getSoluteDielectric`	Get the dielectric constant for the solute.
`setSoluteDielectric`	Set the dielectric constant for the solute.
`getSurfaceAreaEnergy`	Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.
`setSurfaceAreaEnergy`	Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.
`getNonbondedMethod`	Get the method used for handling long range nonbonded interactions.
`setNonbondedMethod`	Set the method used for handling long range nonbonded interactions.
`getCutoffDistance`	Get the cutoff distance (in nm) being used for nonbonded interactions.
`setCutoffDistance`	Set the cutoff distance (in nm) being used for nonbonded interactions.
`updateParametersInContext`	Update the particle parameters in a `Context` to match those stored in this `Force` object.
`usesPeriodicBoundaryConditions`	Returns whether or not this force makes use of periodic boundary conditions.

Enum: NonbondedMethod

NoCutoff	No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly. This necessarily means that periodic boundary conditions cannot be used. This is the default.
CutoffNonPeriodic	Interactions beyond the cutoff distance are ignored.
CutoffPeriodic	Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of each other particle. Interactions beyond the cutoff distance are ignored.

GBSAOBCForce()¶: Create a GBSAOBCForce().

int getNumParticles() const¶: Get the number of particles in the system.

int addParticle(double charge, double radius, double scalingFactor)¶

Add the GBSA 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 GBSA radius of the particle, measured in nm
scalingFactor – the OBC 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 GBSA radius of the particle, measured in nm
scalingFactor – [out] the OBC 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 GBSA radius of the particle, measured in nm
scalingFactor – the OBC 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.

double getSurfaceAreaEnergy() const¶: Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.

void setSurfaceAreaEnergy(double energy)¶: Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.

NonbondedMethod getNonbondedMethod() const¶: Get the method used for handling long range nonbonded interactions.

void setNonbondedMethod(NonbondedMethod method)¶: Set the method used for handling long range nonbonded interactions.

double getCutoffDistance() const¶

Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Returns: the cutoff distance, measured in nm

void setCutoffDistance(double distance)¶

Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use is NoCutoff, this value will have no effect.

Parameters

distance – the cutoff distance, measured in nm

void updateParametersInContext(Context &context)¶

Update the 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 nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context. Furthermore, this method cannot be used to add new particles, only to change the parameters of existing ones.

bool usesPeriodicBoundaryConditions() const¶

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

Returns: true if force uses PBC and false otherwise