OpenMM
|
This class implements an implicit solvation force using the GBSA-OBC model. More...
#include <GBSAOBCForce.h>
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 | |
ForceImpl * | createImpl () const |
When a Context is created, it invokes this method on each Force in the System. | |
Protected Member Functions inherited from Force | |
ForceImpl & | getImplInContext (Context &context) |
Get the ForceImpl corresponding to this Force in a Context. | |
ContextImpl & | getContextImpl (Context &context) |
Get the ContextImpl corresponding to a Context. | |
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.
enum NonbondedMethod |
This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
GBSAOBCForce | ( | ) |
Create a 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 |
|
protectedvirtual |
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.
|
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 |
|
inline |
Get the dielectric constant for the solute.
|
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 |
|
inline |
Set the dielectric constant for the solute.
|
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.