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GBVIForce.h
1 #ifndef OPENMM_GBVIFORCEFIELD_H_
2 #define OPENMM_GBVIFORCEFIELD_H_
3
4 /* -------------------------------------------------------------------------- *
5 * OpenMM *
6 * -------------------------------------------------------------------------- *
7 * This is part of the OpenMM molecular simulation toolkit originating from *
8 * Simbios, the NIH National Center for Physics-Based Simulation of *
9 * Biological Structures at Stanford, funded under the NIH Roadmap for *
10 * Medical Research, grant U54 GM072970. See https://simtk.org. *
11 * *
12 * Portions copyright (c) 2008-2009 Stanford University and the Authors. *
13 * Authors: Peter Eastman *
14 * Contributors: *
15 * *
16 * Permission is hereby granted, free of charge, to any person obtaining a *
17 * copy of this software and associated documentation files (the "Software"), *
18 * to deal in the Software without restriction, including without limitation *
19 * the rights to use, copy, modify, merge, publish, distribute, sublicense, *
20 * and/or sell copies of the Software, and to permit persons to whom the *
21 * Software is furnished to do so, subject to the following conditions: *
22 * *
23 * The above copyright notice and this permission notice shall be included in *
24 * all copies or substantial portions of the Software. *
25 * *
26 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
27 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
28 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
29 * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
30 * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
31 * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
32 * USE OR OTHER DEALINGS IN THE SOFTWARE. *
33 * -------------------------------------------------------------------------- */
34
35 #include "Force.h"
36 #include <vector>
37 #include "internal/windowsExport.h"
38
39 namespace OpenMM {
40
53 class OPENMM_EXPORT GBVIForce : public Force {
54 public:
58 enum NonbondedMethod {
63 NoCutoff = 0,
67 CutoffNonPeriodic = 1,
72 CutoffPeriodic = 2,
73 };
74
78 enum BornRadiusScalingMethod {
82 NoScaling = 0,
86 QuinticSpline = 1
87 };
88
89 /*
90 * Create a GBVIForce.
91 */
92 GBVIForce();
96 int getNumParticles() const {
97 return particles.size();
98 }
108 int addParticle(double charge, double radius, double gamma);
117 void getParticleParameters(int index, double& charge, double& radius, double& gamma) const;
126 void setParticleParameters(int index, double charge, double radius, double gamma);
135 int addBond(int particle1, int particle2, double distance);
136
145 void getBondParameters(int index, int& particle1, int& particle2, double& distance) const;
154 void setBondParameters( int index, int particle1, int particle2, double bondLength);
160 int getNumBonds() const;
161
165 double getSolventDielectric() const {
166 return solventDielectric;
167 }
171 void setSolventDielectric(double dielectric) {
172 solventDielectric = dielectric;
173 }
177 double getSoluteDielectric() const {
178 return soluteDielectric;
179 }
183 void setSoluteDielectric(double dielectric) {
184 soluteDielectric = dielectric;
185 }
189 NonbondedMethod getNonbondedMethod() const;
193 void setNonbondedMethod(NonbondedMethod method);
200 double getCutoffDistance() const;
207 void setCutoffDistance(double distance);
211 BornRadiusScalingMethod getBornRadiusScalingMethod() const;
215 void setBornRadiusScalingMethod( BornRadiusScalingMethod method);
219 double getQuinticLowerLimitFactor() const;
223 void setQuinticLowerLimitFactor(double quinticLowerLimitFactor );
227 double getQuinticUpperBornRadiusLimit() const;
231 void setQuinticUpperBornRadiusLimit(double quinticUpperBornRadiusLimit);
238 bool usesPeriodicBoundaryConditions() const {
239 return nonbondedMethod == GBVIForce::CutoffPeriodic;
240 }
241 protected:
242 ForceImpl* createImpl() const;
243 private:
244 class ParticleInfo;
245 NonbondedMethod nonbondedMethod;
246 double cutoffDistance, solventDielectric, soluteDielectric;
247
248 BornRadiusScalingMethod scalingMethod;
249 double quinticLowerLimitFactor, quinticUpperBornRadiusLimit;
250
251 class BondInfo;
252 std::vector<ParticleInfo> particles;
253 std::vector<BondInfo> bonds;
254 };
255
260 class GBVIForce::ParticleInfo {
261 public:
262 double charge, radius, gamma;
263 ParticleInfo() {
264 charge = radius = gamma = 0.0;
265 }
266 ParticleInfo(double charge, double radius, double gamma) :
267 charge(charge), radius(radius), gamma(gamma) {
268 }
269 };
270
275 class GBVIForce::BondInfo {
276 public:
277 int particle1, particle2;
278 double bondLength;
279 BondInfo() {
280 bondLength = 0.0;
281 particle1 = -1;
282 particle2 = -1;
283 }
284 BondInfo(int atomIndex1, int atomIndex2, double bondLength) :
285 particle1(atomIndex1), particle2(atomIndex2), bondLength(bondLength) {
286 }
287 };
288
289 } // namespace OpenMM
290
291 #endif /*OPENMM_GBVIFORCEFIELD_H_*/
OpenMM::GBVIForce::getSoluteDielectric
double getSoluteDielectric() const
Get the dielectric constant for the solute.
Definition: GBVIForce.h:177
OpenMM::GBVIForce::CutoffPeriodic
Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic...
Definition: GBVIForce.h:72
OpenMM::Force
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
OpenMM::GBVIForce::BornRadiusScalingMethod
BornRadiusScalingMethod
This is an enumeration of the different methods that may be used for scaling of the Born radii...
Definition: GBVIForce.h:78
OpenMM::GBVIForce::usesPeriodicBoundaryConditions
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: GBVIForce.h:238
OpenMM::GBVIForce::setSoluteDielectric
void setSoluteDielectric(double dielectric)
Set the dielectric constant for the solute.
Definition: GBVIForce.h:183
OpenMM::GBVIForce::setSolventDielectric
void setSolventDielectric(double dielectric)
Set the dielectric constant for the solvent.
Definition: GBVIForce.h:171
OpenMM::GBVIForce::getNumParticles
int getNumParticles() const
Get the number of particles in the system.
Definition: GBVIForce.h:96
OpenMM::GBVIForce::getSolventDielectric
double getSolventDielectric() const
Get the dielectric constant for the solvent.
Definition: GBVIForce.h:165
OpenMM
Definition: AndersenThermostat.h:40
OpenMM::GBVIForce
This class implements an implicit solvation force using the GB/VI model.
Definition: GBVIForce.h:53
OpenMM::GBVIForce::NonbondedMethod
NonbondedMethod
This is an enumeration of the different methods that may be used for handling long range nonbonded fo...
Definition: GBVIForce.h:58