This class implements an implicit solvation force using the GBSA-OBC model. More...
#include <GBSAOBCForce.h>
Classes | |
class | ParticleInfo |
This is an internal class used to record information about a particle. | |
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 () | |
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. | |
Protected Member Functions | |
ForceImpl * | createImpl () |
When a Context is created, it invokes this method on each Force in the System. |
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().
enum NonbondedMethod |
This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
GBSAOBCForce | ( | ) |
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.
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 |
ForceImpl* createImpl | ( | ) | [protected, virtual] |
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.
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.
index | the index of the particle for which to get 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 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.
distance | the 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.
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 |
void setSoluteDielectric | ( | double | dielectric | ) | [inline] |
Set the dielectric constant for the solute.
void setSolventDielectric | ( | double | dielectric | ) | [inline] |
Set the dielectric constant for the solvent.