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Public Member Functions
AdAmberForceField Class Reference

#import <AdunAmberForceField.h>

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List of all members.

Public Member Functions

(void) - evaluateEnergiesUsingInteractionsInvolvingElements:
(void) - evaluateForcesDueToElements:
- Public Member Functions inherited from AdMolecularMechanicsForceField
(id) - initWithDictionary:
(id) - init
(id) - initWithSystem:
(id) - initWithSystem:nonbondedTerm:
(id) - initWithSystem:nonbondedTerm:customTerms:
(AdDataMatrix *) - evaluateFiniteDifferenceForcesForTerm:
(void) - evaluateFiniteDifferenceForces
(void) - setSystem:
(void) - setNonbondedTerm:
(AdNonbondedTerm *) - nonbondedTerm
(NSString *) - vdwInteractionType
(void) - logForceSaveMatrix:
(void) - _clearForceSaveMatrix
(void) - _saveForcesForStep:forForce:
(bool) - savesForces
(void) - setOptions:
(NSArray *) - allTerms
(NSArray *) - allEnergies
(NSArray *) - arrayOfEnergiesForTerms:notFoundMarker:
(NSArray *) - arrayOfCoreTermEnergies
(NSDictionary *) - dictionaryOfCoreTermEnergies
(void) - _systemCleanUp
(void) - _updateAccelerations
(void) - _initialisationForSystem
(void) - _createReciprocalMassArray
(void) - _handleSystemContentsChange:
(AdMatrix *) - _internalDataStorageForGroups:parameters:
- Public Member Functions inherited from AdForceField
(void) - evaluateEnergies
(double) - totalEnergy
(void) - evaluateForces
(AdMatrix *) - forces
(void) - setForces:
(AdMatrix *) - accelerations
(void) - setAccelerations:
(void) - clearForces
(id) - system
(id) - availableTerms
- Public Member Functions inherited from
(BOOL) - allowsDirectModificationOfMatrix:
(BOOL) - matrixIsAvailableForModification:
(void) - object:willBeginWritingToMatrix:
(void) - object:didFinishWritingToMatrix:

Additional Inherited Members

- Static Public Member Functions inherited from AdMolecularMechanicsForceField
(id) + forceFieldForSystem:
- Protected Attributes inherited from AdMolecularMechanicsForceField
NSMutableArray * availableTerms
NSArray * coreTerms

Detailed Description

AdMolecularMechanicsForceField subclass representing the amber force field -

\[ U(r) = \sum_{Bonds} \frac{k_{i}}{2}(x - x_{i})^{2} + \sum_{Angles} \frac{k_{i}}{2}(\theta - \theta_{i})^{2} + \sum_{Torsions} k_{i}(1 + cos(n\theta - \phi)) + \sum_{Improper} \frac{k_{i}}{2}(\theta - \theta_{i})^{2} + \sum_{Nonbonded} \left [ \frac{1}{4 \pi \epsilon} \frac{q_{i}q_{j}}{r_{ij}} + \sqrt{\epsilon_{i}\epsilon_{j}} \left \{ \left( \frac{0.5(r_{i}^{*} + r_{j}^{*})}{r_{ij}} \right)^{12} - 2 \left( \frac{0.5(r_{i}^{*} + r_{j}^{*})}{r_{ij}} \right)^{6} \right \} \right ] \]

The following list details the names of the terms along with the associated information that must be provided by the system object that the AdAmberForceField instance operates on.

AdAmberForceField objects use an appropriate AdNonbondedTerm subclass instance to calculate the forces and energies due to the nonbonded terms i.e. the combined Lennard-Jones and ColoumbElectrostatic interactions, which must be supplied separately.


Member Function Documentation

- (void) evaluateEnergiesUsingInteractionsInvolvingElements: (NSIndexSet*)  elementIndexes
Todo:
Not implemented

Implements AdForceField.

- (void) evaluateForcesDueToElements: (NSIndexSet *)  elementIndexes
Todo:
Not implemented

Implements AdForceField.