#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 #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 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_*/