#ifndef OPENMM_GBSAOBCFORCEFIELD_H_
#define OPENMM_GBSAOBCFORCEFIELD_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "Force.h"
#include <vector>
#include "internal/windowsExport.h"
namespace OpenMM {
/**
* 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.
*/
class OPENMM_EXPORT GBSAOBCForce : public Force {
public:
/**
* This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
*/
enum NonbondedMethod {
/**
* 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.
*/
NoCutoff = 0,
/**
* Interactions beyond the cutoff distance are ignored.
*/
CutoffNonPeriodic = 1,
/**
* 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.
*/
CutoffPeriodic = 2,
};
/**
* Create a GBSAOBCForce.
*/
GBSAOBCForce();
/**
* Get the number of particles in the system.
*/
int getNumParticles() const {
return particles.size();
}
/**
* 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.
*
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
* @return the index of the particle that was added
*/
int addParticle(double charge, double radius, double scalingFactor);
/**
* Get the force field parameters for a particle.
*
* @param index the index of the particle for which to get parameters
* @param[out] charge the charge of the particle, measured in units of the proton charge
* @param[out] radius the GBSA radius of the particle, measured in nm
* @param[out] scalingFactor the OBC scaling factor for the particle
*/
void getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const;
/**
* Set the force field parameters for a particle.
*
* @param index the index of the particle for which to set parameters
* @param charge the charge of the particle, measured in units of the proton charge
* @param radius the GBSA radius of the particle, measured in nm
* @param scalingFactor the OBC scaling factor for the particle
*/
void setParticleParameters(int index, double charge, double radius, double scalingFactor);
/**
* Get the dielectric constant for the solvent.
*/
double getSolventDielectric() const {
return solventDielectric;
}
/**
* Set the dielectric constant for the solvent.
*/
void setSolventDielectric(double dielectric) {
solventDielectric = dielectric;
}
/**
* Get the dielectric constant for the solute.
*/
double getSoluteDielectric() const {
return soluteDielectric;
}
/**
* Set the dielectric constant for the solute.
*/
void setSoluteDielectric(double dielectric) {
soluteDielectric = dielectric;
}
/**
* Get the energy scale for the surface energy term, measured in kJ/mol/nm^2.
*/
double getSurfaceAreaEnergy() const {
return surfaceAreaEnergy;
}
/**
* Set the energy scale for the surface energy term, measured in kJ/mol/nm^2.
*/
void setSurfaceAreaEnergy(double energy) {
surfaceAreaEnergy = energy;
}
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
void setNonbondedMethod(NonbondedMethod method);
/**
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @return the cutoff distance, measured in nm
*/
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* is NoCutoff, this value will have no effect.
*
* @param distance the cutoff distance, measured in nm
*/
void setCutoffDistance(double distance);
/**
* 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.
*/
void updateParametersInContext(Context& context);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return nonbondedMethod == GBSAOBCForce::CutoffPeriodic;
}
protected:
ForceImpl* createImpl() const;
private:
class ParticleInfo;
NonbondedMethod nonbondedMethod;
double cutoffDistance, solventDielectric, soluteDielectric, surfaceAreaEnergy;
std::vector<ParticleInfo> particles;
};
/**
* This is an internal class used to record information about a particle.
* @private
*/
class GBSAOBCForce::ParticleInfo {
public:
double charge, radius, scalingFactor;
ParticleInfo() {
charge = radius = scalingFactor = 0.0;
}
ParticleInfo(double charge, double radius, double scalingFactor) :
charge(charge), radius(radius), scalingFactor(scalingFactor) {
}
};
} // namespace OpenMM
#endif /*OPENMM_GBSAOBCFORCEFIELD_H_*/