DuMMForceFieldSubsystem Class Reference
#include <DuMMForceFieldSubsystem.h>
Inheritance diagram for DuMMForceFieldSubsystem:
Detailed Description
This is a concrete subsystem that provides basic molecular mechanics functionality FOR DEMO AND PROOF OF CONCEPT only!!! It is not likely to perform well on anything.UNITS: This subsystem requires that the system be modeled in "MD units" of nanometers, daltons (g/mol), and picoseconds, yielding consistent energy units of kJ/mol==(Da-nm^2/ps^2), and force in kJ/mol-nm. Charge is in proton charge units e, and angles are in radians. For convenience, we allow the force field to be defined in "KA" units, that is, angstroms instead of nanometers, and energy in kcal rather than kJ, and we also allow angles to be supplied in degrees. However, these are immediately converted to the MD units described above.
Public Types | |
| enum | VdwMixingRule { WaldmanHagler = 1, HalgrenHHG = 2, Jorgensen = 3, LorentzBerthelot = 4, Kong = 5 } |
Public Member Functions | |
| const char * | getVdwMixingRuleName (VdwMixingRule) const |
| DuMMForceFieldSubsystem () | |
| DuMMForceFieldSubsystem (MolecularMechanicsSystem &) | |
| DuMM::AtomIndex | addAtom (DuMM::ChargedAtomTypeIndex chargedAtomTypeIx) |
| DuMM::BondIndex | addBond (DuMM::AtomIndex atom1Ix, DuMM::AtomIndex atom2Ix) |
| int | getNAtoms () const |
| Real | getAtomMass (DuMM::AtomIndex atomIx) const |
| int | getAtomElement (DuMM::AtomIndex atomIx) const |
| Real | getAtomRadius (DuMM::AtomIndex atomIx) const |
| Vec3 | getAtomStationOnBody (DuMM::AtomIndex atomIx) const |
| Vec3 | getAtomStationInCluster (DuMM::AtomIndex atomIx, DuMM::ClusterIndex clusterIx) const |
| MobilizedBodyIndex | getAtomBody (DuMM::AtomIndex atomIx) const |
| Vec3 | getElementDefaultColor (int atomicNumber) const |
| Vec3 | getAtomDefaultColor (DuMM::AtomIndex atomIx) const |
| int | getNBonds () const |
| DuMM::AtomIndex | getBondAtom (DuMM::BondIndex bond, int which) const |
| DuMM::ClusterIndex | createCluster (const char *clusterName) |
| void | placeAtomInCluster (DuMM::AtomIndex atomIx, DuMM::ClusterIndex clusterIx, const Vec3 &station) |
| void | placeClusterInCluster (DuMM::ClusterIndex childClusterIndex, DuMM::ClusterIndex parentClusterIndex, const Transform &placement) |
| MassProperties | calcClusterMassProperties (DuMM::ClusterIndex clusterIx, const Transform &=Transform()) const |
| MobilizedBodyIndex | getClusterBody (DuMM::ClusterIndex clusterIx) const |
| Transform | getClusterPlacementOnBody (DuMM::ClusterIndex clusterIx) const |
| Transform | getClusterPlacementInCluster (DuMM::ClusterIndex childClusterIndex, DuMM::ClusterIndex parentClusterIndex) const |
| void | attachClusterToBody (DuMM::ClusterIndex clusterIx, MobilizedBodyIndex body, const Transform &=Transform()) |
| void | attachAtomToBody (DuMM::AtomIndex atomIx, MobilizedBodyIndex body, const Vec3 &station=Vec3(0)) |
| void | dumpCForceFieldParameters (std::ostream &os, const String &methodName="loadParameters") const |
| void | defineAtomClass (DuMM::AtomClassIndex atomClassIx, const char *atomClassName, int elementNumber, int expectedValence, Real vdwRadiusInNm, Real vdwWellDepthInKJ) |
| void | defineAtomClass_KA (DuMM::AtomClassIndex atomClassIx, const char *atomClassName, int element, int valence, Real vdwRadiusInAng, Real vdwWellDepthInKcal) |
| void | defineAtomClass_KA (int atomClassIx, const char *atomClassName, int element, int valence, Real vdwRadiusInAng, Real vdwWellDepthInKcal) |
| bool | hasAtomClass (DuMM::AtomClassIndex) const |
| bool | hasAtomClass (const String &atomClassName) const |
| DuMM::AtomClassIndex | getAtomClassIndex (const String &atomClassName) const |
| DuMM::AtomClassIndex | getNextUnusedAtomClassIndex () const |
| DuMM::AtomClassIndex | getAtomClassIndex (DuMM::AtomIndex atomIx) const |
| Real | getVdwRadius (DuMM::AtomClassIndex atomClassIx) const |
| Real | getVdwWellDepth (DuMM::AtomClassIndex atomClassIx) const |
| void | defineChargedAtomType (DuMM::ChargedAtomTypeIndex atomTypeIx, const char *atomTypeName, DuMM::AtomClassIndex atomClassIx, Real partialChargeInE) |
| void | defineChargedAtomType_KA (DuMM::ChargedAtomTypeIndex atomTypeIx, const char *atomTypeName, DuMM::AtomClassIndex atomClassIx, Real partialChargeInE) |
| void | defineChargedAtomType_KA (int atomTypeIx, const char *atomTypeName, int atomClassIx, Real partialChargeInE) |
| bool | hasChargedAtomType (DuMM::ChargedAtomTypeIndex) const |
| bool | hasChargedAtomType (const String &chargedTypeName) const |
| DuMM::ChargedAtomTypeIndex | getChargedAtomTypeIndex (const String &chargedTypeName) const |
| DuMM::ChargedAtomTypeIndex | getNextUnusedChargedAtomTypeIndex () const |
| void | defineBondStretch (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, Real stiffnessInKJperNmSq, Real nominalLengthInNm) |
| void | defineBondStretch_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, Real stiffnessInKcalPerAngSq, Real nominalLengthInAng) |
| void | defineBondStretch_KA (int class1, int class2, Real stiffnessInKcalPerAngSq, Real nominalLengthInAng) |
| void | defineBondBend (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, Real stiffnessInKJPerRadSq, Real nominalAngleInDeg) |
| void | defineBondBend_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, Real stiffnessInKcalPerRadSq, Real nominalAngleInDeg) |
| void | defineBondBend_KA (int class1, int class2, int class3, Real stiffnessInKcalPerRadSq, Real nominalAngleInDeg) |
| void | defineBondTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees) |
| void | defineBondTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees) |
| void | defineBondTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees, int periodicity3, Real amp3InKJ, Real phase3InDegrees) |
| void | defineBondTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) |
| void | defineBondTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) |
| void | defineBondTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) |
| void | defineBondTorsion_KA (int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) |
| void | defineBondTorsion_KA (int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) |
| void | defineBondTorsion_KA (int class1, int class2, int class3, int class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) |
| void | defineAmberImproperTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees) |
| void | defineAmberImproperTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees) |
| void | defineAmberImproperTorsion (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKJ, Real phase1InDegrees, int periodicity2, Real amp2InKJ, Real phase2InDegrees, int periodicity3, Real amp3InKJ, Real phase3InDegrees) |
| void | defineAmberImproperTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees) |
| void | defineAmberImproperTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees) |
| void | defineAmberImproperTorsion_KA (DuMM::AtomClassIndex class1, DuMM::AtomClassIndex class2, DuMM::AtomClassIndex class3, DuMM::AtomClassIndex class4, int periodicity1, Real amp1InKcal, Real phase1InDegrees, int periodicity2, Real amp2InKcal, Real phase2InDegrees, int periodicity3, Real amp3InKcal, Real phase3InDegrees) |
| void | setVdwMixingRule (VdwMixingRule) |
| VdwMixingRule | getVdwMixingRule () const |
| void | setVdw12ScaleFactor (Real) |
| void | setVdw13ScaleFactor (Real) |
| void | setVdw14ScaleFactor (Real) |
| void | setVdw15ScaleFactor (Real) |
| void | setCoulomb12ScaleFactor (Real) |
| void | setCoulomb13ScaleFactor (Real) |
| void | setCoulomb14ScaleFactor (Real) |
| void | setCoulomb15ScaleFactor (Real) |
| void | setVdwGlobalScaleFactor (Real) |
| void | setCoulombGlobalScaleFactor (Real) |
| void | setBondStretchGlobalScaleFactor (Real) |
| void | setBondBendGlobalScaleFactor (Real) |
| void | setBondTorsionGlobalScaleFactor (Real) |
| void | setAmberImproperTorsionGlobalScaleFactor (Real) |
| void | setGbsaGlobalScaleFactor (Real) |
| void | setGbsaIncludeAceApproximation (bool) |
| void | setGbsaIncludeAceApproximationOn () |
| void | setGbsaIncludeAceApproximationOff () |
| Real | getVdwGlobalScaleFactor () const |
| void | setAllGlobalScaleFactors (Real s) |
| bool | getUseMultithreadedComputation () |
| void | setUseMultithreadedComputation (bool) |
| long int | getForceEvaluationCount () const |
| void | dump () const |
| void | loadAmber99Parameters () |
| Use Amber99 force field parameters. | |
| void | populateFromTinkerParameterFile (std::istream &) |
| Load force field paramters from a TINKER format force field parameter file. | |
| void | setBiotypeChargedAtomType (DuMM::ChargedAtomTypeIndex chargedAtomTypeIndex, BiotypeIndex biotypeIx) |
| Associate a biotype with a ChargedAtomType in this subsystem. | |
| DuMM::ChargedAtomTypeIndex | getBiotypeChargedAtomType (BiotypeIndex biotypeIx) const |
| get charged atom type index in this force field associated with a particular Biotype | |
| std::ostream & | generateBiotypeChargedAtomTypeSelfCode (std::ostream &os) const |
| void | loadTestMoleculeParameters () |
Protected Member Functions | |
| void | defineIncompleteAtomClass (DuMM::AtomClassIndex classIx, const char *name, int elementNumber, int valence) |
| void | defineIncompleteAtomClass_KA (DuMM::AtomClassIndex classIx, const char *name, int elementNumber, int valence) |
| void | setAtomClassVdwParameters (DuMM::AtomClassIndex atomClassIx, Real vdwRadiusInNm, Real vdwWellDepthInKJPerMol) |
| void | setAtomClassVdwParameters_KA (DuMM::AtomClassIndex atomClassIx, Real radiusInAng, Real wellDepthInKcal) |
| bool | isValidAtomClass (DuMM::AtomClassIndex) const |
| void | defineIncompleteChargedAtomType (DuMM::ChargedAtomTypeIndex typeIx, const char *name, DuMM::AtomClassIndex classIx) |
| void | defineIncompleteChargedAtomType_KA (DuMM::ChargedAtomTypeIndex typeIx, const char *name, DuMM::AtomClassIndex classIx) |
| void | setChargedAtomTypeCharge (DuMM::ChargedAtomTypeIndex, Real charge) |
| void | setChargedAtomTypeCharge_KA (DuMM::ChargedAtomTypeIndex chargedAtomTypeIx, Real charge) |
Protected Attributes | |
| DuMMForceFieldSubsystem | |
| ForceSubsystem | |
| Subsystem | |
Friends | |
| class | MolecularMechanicsSystem |
Member Enumeration Documentation
| enum VdwMixingRule |
Constructor & Destructor Documentation
| DuMMForceFieldSubsystem | ( | MolecularMechanicsSystem & | ) | [explicit] |
Member Function Documentation
| const char* getVdwMixingRuleName | ( | VdwMixingRule | ) | const |
| DuMM::AtomIndex addAtom | ( | DuMM::ChargedAtomTypeIndex | chargedAtomTypeIx | ) |
| DuMM::BondIndex addBond | ( | DuMM::AtomIndex | atom1Ix, | |
| DuMM::AtomIndex | atom2Ix | |||
| ) |
| int getNAtoms | ( | ) | const |
| Real getAtomMass | ( | DuMM::AtomIndex | atomIx | ) | const |
| int getAtomElement | ( | DuMM::AtomIndex | atomIx | ) | const |
| Real getAtomRadius | ( | DuMM::AtomIndex | atomIx | ) | const |
| Vec3 getAtomStationOnBody | ( | DuMM::AtomIndex | atomIx | ) | const |
| Vec3 getAtomStationInCluster | ( | DuMM::AtomIndex | atomIx, | |
| DuMM::ClusterIndex | clusterIx | |||
| ) | const |
| MobilizedBodyIndex getAtomBody | ( | DuMM::AtomIndex | atomIx | ) | const |
| Vec3 getElementDefaultColor | ( | int | atomicNumber | ) | const |
| Vec3 getAtomDefaultColor | ( | DuMM::AtomIndex | atomIx | ) | const |
| int getNBonds | ( | ) | const |
| DuMM::AtomIndex getBondAtom | ( | DuMM::BondIndex | bond, | |
| int | which | |||
| ) | const |
| DuMM::ClusterIndex createCluster | ( | const char * | clusterName | ) |
| void placeAtomInCluster | ( | DuMM::AtomIndex | atomIx, | |
| DuMM::ClusterIndex | clusterIx, | |||
| const Vec3 & | station | |||
| ) |
| void placeClusterInCluster | ( | DuMM::ClusterIndex | childClusterIndex, | |
| DuMM::ClusterIndex | parentClusterIndex, | |||
| const Transform & | placement | |||
| ) |
| MassProperties calcClusterMassProperties | ( | DuMM::ClusterIndex | clusterIx, | |
| const Transform & | = Transform() | |||
| ) | const |
| MobilizedBodyIndex getClusterBody | ( | DuMM::ClusterIndex | clusterIx | ) | const |
| Transform getClusterPlacementOnBody | ( | DuMM::ClusterIndex | clusterIx | ) | const |
| Transform getClusterPlacementInCluster | ( | DuMM::ClusterIndex | childClusterIndex, | |
| DuMM::ClusterIndex | parentClusterIndex | |||
| ) | const |
| void attachClusterToBody | ( | DuMM::ClusterIndex | clusterIx, | |
| MobilizedBodyIndex | body, | |||
| const Transform & | = Transform() | |||
| ) |
| void attachAtomToBody | ( | DuMM::AtomIndex | atomIx, | |
| MobilizedBodyIndex | body, | |||
| const Vec3 & | station = Vec3(0) | |||
| ) |
| void dumpCForceFieldParameters | ( | std::ostream & | os, | |
| const String & | methodName = "loadParameters" | |||
| ) | const |
| void defineAtomClass | ( | DuMM::AtomClassIndex | atomClassIx, | |
| const char * | atomClassName, | |||
| int | elementNumber, | |||
| int | expectedValence, | |||
| Real | vdwRadiusInNm, | |||
| Real | vdwWellDepthInKJ | |||
| ) | [inline] |
| void defineAtomClass_KA | ( | DuMM::AtomClassIndex | atomClassIx, | |
| const char * | atomClassName, | |||
| int | element, | |||
| int | valence, | |||
| Real | vdwRadiusInAng, | |||
| Real | vdwWellDepthInKcal | |||
| ) | [inline] |
Referenced by main(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Water::Water().
| void defineAtomClass_KA | ( | int | atomClassIx, | |
| const char * | atomClassName, | |||
| int | element, | |||
| int | valence, | |||
| Real | vdwRadiusInAng, | |||
| Real | vdwWellDepthInKcal | |||
| ) | [inline] |
| bool hasAtomClass | ( | DuMM::AtomClassIndex | ) | const |
Referenced by ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Water::Water().
| bool hasAtomClass | ( | const String & | atomClassName | ) | const |
| DuMM::AtomClassIndex getAtomClassIndex | ( | const String & | atomClassName | ) | const |
Referenced by main(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Propane::setAmberLikeParameters().
| DuMM::AtomClassIndex getNextUnusedAtomClassIndex | ( | ) | const |
Referenced by main(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), and LithiumIon::setAmberLikeParameters().
| DuMM::AtomClassIndex getAtomClassIndex | ( | DuMM::AtomIndex | atomIx | ) | const |
| Real getVdwRadius | ( | DuMM::AtomClassIndex | atomClassIx | ) | const |
| Real getVdwWellDepth | ( | DuMM::AtomClassIndex | atomClassIx | ) | const |
| void defineChargedAtomType | ( | DuMM::ChargedAtomTypeIndex | atomTypeIx, | |
| const char * | atomTypeName, | |||
| DuMM::AtomClassIndex | atomClassIx, | |||
| Real | partialChargeInE | |||
| ) | [inline] |
Referenced by main(), P12::P12(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), Propane::setAmberLikeParameters(), and Water::Water().
| void defineChargedAtomType_KA | ( | DuMM::ChargedAtomTypeIndex | atomTypeIx, | |
| const char * | atomTypeName, | |||
| DuMM::AtomClassIndex | atomClassIx, | |||
| Real | partialChargeInE | |||
| ) | [inline] |
| void defineChargedAtomType_KA | ( | int | atomTypeIx, | |
| const char * | atomTypeName, | |||
| int | atomClassIx, | |||
| Real | partialChargeInE | |||
| ) | [inline] |
| bool hasChargedAtomType | ( | DuMM::ChargedAtomTypeIndex | ) | const |
Referenced by P12::P12(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Water::Water().
| bool hasChargedAtomType | ( | const String & | chargedTypeName | ) | const |
| DuMM::ChargedAtomTypeIndex getChargedAtomTypeIndex | ( | const String & | chargedTypeName | ) | const |
Referenced by main(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Propane::setAmberLikeParameters().
| DuMM::ChargedAtomTypeIndex getNextUnusedChargedAtomTypeIndex | ( | ) | const |
Referenced by main(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), and Propane::setAmberLikeParameters().
| void defineBondStretch | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| Real | stiffnessInKJperNmSq, | |||
| Real | nominalLengthInNm | |||
| ) |
| void defineBondStretch_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| Real | stiffnessInKcalPerAngSq, | |||
| Real | nominalLengthInAng | |||
| ) | [inline] |
References SimTK::square().
| void defineBondStretch_KA | ( | int | class1, | |
| int | class2, | |||
| Real | stiffnessInKcalPerAngSq, | |||
| Real | nominalLengthInAng | |||
| ) | [inline] |
| void defineBondBend | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| Real | stiffnessInKJPerRadSq, | |||
| Real | nominalAngleInDeg | |||
| ) |
| void defineBondBend_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| Real | stiffnessInKcalPerRadSq, | |||
| Real | nominalAngleInDeg | |||
| ) | [inline] |
| void defineBondBend_KA | ( | int | class1, | |
| int | class2, | |||
| int | class3, | |||
| Real | stiffnessInKcalPerRadSq, | |||
| Real | nominalAngleInDeg | |||
| ) | [inline] |
| void defineBondTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees | |||
| ) |
| void defineBondTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKJ, | |||
| Real | phase2InDegrees | |||
| ) |
| void defineBondTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKJ, | |||
| Real | phase2InDegrees, | |||
| int | periodicity3, | |||
| Real | amp3InKJ, | |||
| Real | phase3InDegrees | |||
| ) |
| void defineBondTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees | |||
| ) | [inline] |
| void defineBondTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees | |||
| ) | [inline] |
| void defineBondTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees, | |||
| int | periodicity3, | |||
| Real | amp3InKcal, | |||
| Real | phase3InDegrees | |||
| ) | [inline] |
| void defineBondTorsion_KA | ( | int | class1, | |
| int | class2, | |||
| int | class3, | |||
| int | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees | |||
| ) | [inline] |
| void defineBondTorsion_KA | ( | int | class1, | |
| int | class2, | |||
| int | class3, | |||
| int | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees | |||
| ) | [inline] |
| void defineBondTorsion_KA | ( | int | class1, | |
| int | class2, | |||
| int | class3, | |||
| int | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees, | |||
| int | periodicity3, | |||
| Real | amp3InKcal, | |||
| Real | phase3InDegrees | |||
| ) | [inline] |
| void defineAmberImproperTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees | |||
| ) |
| void defineAmberImproperTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKJ, | |||
| Real | phase2InDegrees | |||
| ) |
| void defineAmberImproperTorsion | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKJ, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKJ, | |||
| Real | phase2InDegrees, | |||
| int | periodicity3, | |||
| Real | amp3InKJ, | |||
| Real | phase3InDegrees | |||
| ) |
| void defineAmberImproperTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees | |||
| ) | [inline] |
| void defineAmberImproperTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees | |||
| ) | [inline] |
| void defineAmberImproperTorsion_KA | ( | DuMM::AtomClassIndex | class1, | |
| DuMM::AtomClassIndex | class2, | |||
| DuMM::AtomClassIndex | class3, | |||
| DuMM::AtomClassIndex | class4, | |||
| int | periodicity1, | |||
| Real | amp1InKcal, | |||
| Real | phase1InDegrees, | |||
| int | periodicity2, | |||
| Real | amp2InKcal, | |||
| Real | phase2InDegrees, | |||
| int | periodicity3, | |||
| Real | amp3InKcal, | |||
| Real | phase3InDegrees | |||
| ) | [inline] |
| void setVdwMixingRule | ( | VdwMixingRule | ) |
| VdwMixingRule getVdwMixingRule | ( | ) | const |
| void setVdw12ScaleFactor | ( | Real | ) |
| void setVdw13ScaleFactor | ( | Real | ) |
| void setVdw14ScaleFactor | ( | Real | ) |
| void setVdw15ScaleFactor | ( | Real | ) |
| void setCoulomb12ScaleFactor | ( | Real | ) |
| void setCoulomb13ScaleFactor | ( | Real | ) |
| void setCoulomb14ScaleFactor | ( | Real | ) |
| void setCoulomb15ScaleFactor | ( | Real | ) |
| void setVdwGlobalScaleFactor | ( | Real | ) |
Referenced by main().
| void setCoulombGlobalScaleFactor | ( | Real | ) |
Referenced by main().
| void setBondStretchGlobalScaleFactor | ( | Real | ) |
| void setBondBendGlobalScaleFactor | ( | Real | ) |
| void setBondTorsionGlobalScaleFactor | ( | Real | ) |
| void setAmberImproperTorsionGlobalScaleFactor | ( | Real | ) |
| void setGbsaGlobalScaleFactor | ( | Real | ) |
Referenced by main().
| void setGbsaIncludeAceApproximation | ( | bool | ) |
| void setGbsaIncludeAceApproximationOn | ( | ) | [inline] |
| void setGbsaIncludeAceApproximationOff | ( | ) | [inline] |
| Real getVdwGlobalScaleFactor | ( | ) | const |
| void setAllGlobalScaleFactors | ( | Real | s | ) | [inline] |
| bool getUseMultithreadedComputation | ( | ) |
Referenced by main().
| void setUseMultithreadedComputation | ( | bool | ) |
Referenced by main().
| long int getForceEvaluationCount | ( | ) | const |
Referenced by integrate().
| void dump | ( | ) | const |
| void loadAmber99Parameters | ( | ) |
Use Amber99 force field parameters.
This way you don't need to load the parameters from a file.
Referenced by Amber99ForceSubsystem::Amber99ForceSubsystem(), integrate(), and main().
| void populateFromTinkerParameterFile | ( | std::istream & | ) |
Load force field paramters from a TINKER format force field parameter file.
Only the Amber99 force field is tested
Referenced by main().
| void setBiotypeChargedAtomType | ( | DuMM::ChargedAtomTypeIndex | chargedAtomTypeIndex, | |
| BiotypeIndex | biotypeIx | |||
| ) |
Associate a biotype with a ChargedAtomType in this subsystem.
A Biotype association is required for every Biotype found on atoms in the current System
- Parameters:
-
chargedAtomTypeIndex Prexisting charged atom type index in this subsystem biotypeIx Preexisting BiotypeIndex defined in the Biotype class
Referenced by main(), P12::P12(), ChlorideIon::setAmberLikeParameters(), ZincIon::setAmberLikeParameters(), CalciumIon::setAmberLikeParameters(), MagnesiumIon::setAmberLikeParameters(), CesiumIon::setAmberLikeParameters(), RubidiumIon::setAmberLikeParameters(), PotassiumIon::setAmberLikeParameters(), SodiumIon::setAmberLikeParameters(), LithiumIon::setAmberLikeParameters(), Propane::setAmberLikeParameters(), and Water::Water().
| DuMM::ChargedAtomTypeIndex getBiotypeChargedAtomType | ( | BiotypeIndex | biotypeIx | ) | const |
get charged atom type index in this force field associated with a particular Biotype
| std::ostream& generateBiotypeChargedAtomTypeSelfCode | ( | std::ostream & | os | ) | const |
| void loadTestMoleculeParameters | ( | ) |
| void defineIncompleteAtomClass | ( | DuMM::AtomClassIndex | classIx, | |
| const char * | name, | |||
| int | elementNumber, | |||
| int | valence | |||
| ) | [protected] |
| void defineIncompleteAtomClass_KA | ( | DuMM::AtomClassIndex | classIx, | |
| const char * | name, | |||
| int | elementNumber, | |||
| int | valence | |||
| ) | [inline, protected] |
| void setAtomClassVdwParameters | ( | DuMM::AtomClassIndex | atomClassIx, | |
| Real | vdwRadiusInNm, | |||
| Real | vdwWellDepthInKJPerMol | |||
| ) | [protected] |
| void setAtomClassVdwParameters_KA | ( | DuMM::AtomClassIndex | atomClassIx, | |
| Real | radiusInAng, | |||
| Real | wellDepthInKcal | |||
| ) | [inline, protected] |
| bool isValidAtomClass | ( | DuMM::AtomClassIndex | ) | const [protected] |
| void defineIncompleteChargedAtomType | ( | DuMM::ChargedAtomTypeIndex | typeIx, | |
| const char * | name, | |||
| DuMM::AtomClassIndex | classIx | |||
| ) | [protected] |
| void defineIncompleteChargedAtomType_KA | ( | DuMM::ChargedAtomTypeIndex | typeIx, | |
| const char * | name, | |||
| DuMM::AtomClassIndex | classIx | |||
| ) | [inline, protected] |
| void setChargedAtomTypeCharge | ( | DuMM::ChargedAtomTypeIndex | , | |
| Real | charge | |||
| ) | [protected] |
| void setChargedAtomTypeCharge_KA | ( | DuMM::ChargedAtomTypeIndex | chargedAtomTypeIx, | |
| Real | charge | |||
| ) | [inline, protected] |
Friends And Related Function Documentation
friend class MolecularMechanicsSystem [friend] |
Member Data Documentation
DuMMForceFieldSubsystem [protected] |
ForceSubsystem [protected] |
Reimplemented from ForceSubsystem.
Subsystem [protected] |
Reimplemented from ForceSubsystem.
The documentation for this class was generated from the following file:
