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GBSAOBCForce Class Reference

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

#include <GBSAOBCForce.h>

+ Inheritance diagram for GBSAOBCForce:

Public Types

enum  NonbondedMethod { NoCutoff = 0, CutoffNonPeriodic = 1, CutoffPeriodic = 2 }
 This is an enumeration of the different methods that may be used for handling long range nonbonded forces. More...
 

Public Member Functions

 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.
 
void getParticleParameters (int index, double &charge, double &radius, double &scalingFactor) const
 Get the force field parameters for a particle.
 
void setParticleParameters (int index, double charge, double radius, double scalingFactor)
 Set the force field parameters for a 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.
 
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.
 
void setCutoffDistance (double distance)
 Set the cutoff distance (in nm) being used for nonbonded interactions.
 
void updateParametersInContext (Context &context)
 Update the particle parameters in a Context to match those stored in this Force object.
 
- Public Member Functions inherited from Force
 Force ()
 
virtual ~Force ()
 
int getForceGroup () const
 Get the force group this Force belongs to.
 
void setForceGroup (int group)
 Set the force group this Force belongs to.
 

Protected Member Functions

ForceImplcreateImpl () const
 When a Context is created, it invokes this method on each Force in the System.
 
- Protected Member Functions inherited from Force
ForceImplgetImplInContext (Context &context)
 Get the ForceImpl corresponding to this Force in a Context.
 
ContextImplgetContextImpl (Context &context)
 Get the ContextImpl corresponding to a Context.
 

Detailed Description

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.

Member Enumeration Documentation

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

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.

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.

Constructor & Destructor Documentation

Create a GBSAOBCForce.

Member Function Documentation

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
chargethe charge of the particle, measured in units of the proton charge
radiusthe GBSA radius of the particle, measured in nm
scalingFactorthe OBC scaling factor for the particle
Returns
the index of the particle that was added
ForceImpl* createImpl ( ) const
protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

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
NonbondedMethod getNonbondedMethod ( ) const

Get the method used for handling long range nonbonded interactions.

int getNumParticles ( ) const
inline

Get the number of particles in the system.

void getParticleParameters ( int  index,
double &  charge,
double &  radius,
double &  scalingFactor 
) const

Get the force field parameters for a particle.

Parameters
indexthe index of the particle for which to get parameters
chargethe charge of the particle, measured in units of the proton charge
radiusthe GBSA radius of the particle, measured in nm
scalingFactorthe OBC scaling factor for the particle
double getSoluteDielectric ( ) const
inline

Get the dielectric constant for the solute.

double getSolventDielectric ( ) const
inline

Get the dielectric constant for the solvent.

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
distancethe cutoff distance, measured in nm
void setNonbondedMethod ( NonbondedMethod  method)

Set the method used for handling long range nonbonded interactions.

void setParticleParameters ( int  index,
double  charge,
double  radius,
double  scalingFactor 
)

Set the force field parameters for a particle.

Parameters
indexthe index of the particle for which to set parameters
chargethe charge of the particle, measured in units of the proton charge
radiusthe GBSA radius of the particle, measured in nm
scalingFactorthe OBC scaling factor for the particle
void setSoluteDielectric ( double  dielectric)
inline

Set the dielectric constant for the solute.

void setSolventDielectric ( double  dielectric)
inline

Set the dielectric constant for the solvent.

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 updateParametersInState() 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.


The documentation for this class was generated from the following file: