#import <AdunEnzymixForceField.h>

Inheritance diagram for AdEnzymixForceField:

Collaboration diagram for AdEnzymixForceField:

Public Member Functions
(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
(void)	- evaluateEnergiesUsingInteractionsInvolvingElements:
(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 enzymix force field -

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

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

HarmonicBond - Groups and parameters (Separation & Constant)
HarmonicAngle - Groups and parameters (Angle & Constant)
FourierTorsion - Groups and parameters (Constant, Periodicity & Phase)
HarmonicImproperTorsion - Groups and parameters (Angle & Constant)
Lennard Jones A - See AdNonbondedTerm for more.
ColumbElectrostatic - See AdNonbondedTerm for more.

AdEnzymixForceField 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) evaluateForcesDueToElements: (NSIndexSet *) elementIndexes

Todo:: Not implemented

Implements AdForceField.

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation