/* Portions copyright (c) 2006 Stanford University and Simbios. * Contributors: Pande Group * * 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. */ #ifndef __ReferenceGBVI_H__ #define __ReferenceGBVI_H__ #include #include "RealVec.h" #include "GBVIParameters.h" namespace OpenMM { class ReferenceGBVI { private: // GB/VI parameters GBVIParameters* _gbviParameters; std::vector _switchDeriviative; public: /**--------------------------------------------------------------------------------------- Constructor @param implicitSolventParameters ImplicitSolventParameters reference @return CpuImplicitSolvent object --------------------------------------------------------------------------------------- */ ReferenceGBVI(GBVIParameters* gbviParameters); /**--------------------------------------------------------------------------------------- Destructor --------------------------------------------------------------------------------------- */ ~ReferenceGBVI(); /**--------------------------------------------------------------------------------------- Return GBVIParameters @return GBVIParameters --------------------------------------------------------------------------------------- */ GBVIParameters* getGBVIParameters() const; /**--------------------------------------------------------------------------------------- Set ImplicitSolventParameters @param ImplicitSolventParameters --------------------------------------------------------------------------------------- */ void setGBVIParameters(GBVIParameters* gbviParameters); /**--------------------------------------------------------------------------------------- Get Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008]) @param atomCoordinates atomic coordinates @param bornRadii output array of Born radii @param gbviChain not used --------------------------------------------------------------------------------------- */ void computeBornRadii(const std::vector& atomCoordinates, std::vector& bornRadii); /**--------------------------------------------------------------------------------------- Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return volume --------------------------------------------------------------------------------------- */ static RealOpenMM getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S); /**--------------------------------------------------------------------------------------- Get L (analytical solution for volume integrals) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM getL(RealOpenMM r, RealOpenMM x, RealOpenMM S); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt r @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt x @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S); /**--------------------------------------------------------------------------------------- Sgb function @param t r*r*G_i*G_j @return Sgb (p. 1694 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM Sgb(RealOpenMM t); /**--------------------------------------------------------------------------------------- Get GB/VI energy @param atomCoordinates atomic coordinates @param partialCharges partial charges @return energy --------------------------------------------------------------------------------------- */ RealOpenMM computeBornEnergy(const std::vector& atomCoordinates, const std::vector& partialCharges); /**--------------------------------------------------------------------------------------- Get GB/VI forces @param atomCoordinates atomic coordinates @param partialCharges partial charges @param forces output forces --------------------------------------------------------------------------------------- */ void computeBornForces(std::vector& atomCoordinates, const std::vector& partialCharges, std::vector& inputForces); /**--------------------------------------------------------------------------------------- Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return volume --------------------------------------------------------------------------------------- */ static double getVolumeD(double r, double R, double S); /**--------------------------------------------------------------------------------------- Get L (analytical solution for volume integrals) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double getLD(double r, double x, double S); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt r @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double dL_drD(double r, double x, double S); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt x @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double dL_dxD(double r, double x, double S); /**--------------------------------------------------------------------------------------- Return OBC chain derivative: size = _obcParameters->getNumberOfAtoms() On first call, memory for array is allocated if not set @return array --------------------------------------------------------------------------------------- */ std::vector& getSwitchDeriviative(); /**--------------------------------------------------------------------------------------- Compute quintic spline value and associated derviative @param x value to compute spline at @param rl lower cutoff value @param ru upper cutoff value @param outValue value of spline at x @param outDerivative value of derivative of spline at x --------------------------------------------------------------------------------------- */ void quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru, RealOpenMM* outValue, RealOpenMM* outDerivative); /**--------------------------------------------------------------------------------------- Compute Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008]) and quintic splice switching function @param atomicRadius3 atomic radius cubed @param bornSum Born sum (volume integral) @param gbviParameters Gbvi parameters (parameters used in spline QuinticLowerLimitFactor & QuinticUpperBornRadiusLimit) @param bornRadius output Born radius @param switchDeriviative output switching function deriviative --------------------------------------------------------------------------------------- */ void computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum, GBVIParameters* gbviParameters, RealOpenMM* bornRadius, RealOpenMM* switchDeriviative); }; } // namespace OpenMM #endif // __ReferenceGBVI_H__