GBSAOBCForce

class GBSAOBCForce : public OpenMM::Force

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.

Public Types

enum NonbondedMethod

This is an enumeration of the different methods that may be used for handling long range nonbonded forces.

Values:

enumerator 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.

enumerator CutoffNonPeriodic

Interactions beyond the cutoff distance are ignored.

enumerator 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.

Public Functions

GBSAOBCForce()

Create a GBSAOBCForce.

inline 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

inline double getSolventDielectric() const

Get the dielectric constant for the solvent.

inline void setSolventDielectric(double dielectric)

Set the dielectric constant for the solvent.

inline double getSoluteDielectric() const

Get the dielectric constant for the solute.

inline void setSoluteDielectric(double dielectric)

Set the dielectric constant for the solute.

inline double getSurfaceAreaEnergy() const

Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.

inline 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.

inline virtual bool usesPeriodicBoundaryConditions() const

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

Returns

true if force uses PBC and false otherwise