This class implements the Amoeba torsion-torsion interaction. More...

#include <AmoebaTorsionTorsionForce.h>

Inheritance diagram for AmoebaTorsionTorsionForce:

Public Member Functions
	AmoebaTorsionTorsionForce (void)
	Create an AmoebaTorsionTorsionForce. More...

int	getNumTorsionTorsions (void) const
	Get the number of torsion-torsion terms in the potential function. More...

int	getNumTorsionTorsionGrids (void) const
	Get the number of torsion-torsion grids. More...

int	addTorsionTorsion (int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)
	Add a torsion-torsion term to the force field. More...

void	getTorsionTorsionParameters (int index, int &particle1, int &particle2, int &particle3, int &particle4, int &particle5, int &chiralCheckAtomIndex, int &gridIndex) const
	Get the force field parameters for a torsion-torsion term. More...

void	setTorsionTorsionParameters (int index, int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex)
	Set the force field parameters for a torsion-torsion term. More...

const std::vector< std::vector < std::vector< double > > > &	getTorsionTorsionGrid (int index) const
	Get the torsion-torsion grid at the specified index. More...

void	setTorsionTorsionGrid (int index, const std::vector< std::vector< std::vector< double > > > &grid)
	Set the torsion-torsion grid at the specified index. More...

bool	usesPeriodicBoundaryConditions () const
	Returns whether or not this force makes use of periodic boundary conditions. More...

Public Member Functions inherited from Force
	Force ()

virtual	~Force ()

int	getForceGroup () const
	Get the force group this Force belongs to. More...

void	setForceGroup (int group)
	Set the force group this Force belongs to. More...

Protected Member Functions
ForceImpl *	createImpl () const
	When a Context is created, it invokes this method on each Force in the System. More...

Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context. More...

ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context. More...

Detailed Description

This class implements the Amoeba torsion-torsion interaction.

To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion. After a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().

Constructor & Destructor Documentation

AmoebaTorsionTorsionForce ( void )

Create an AmoebaTorsionTorsionForce.

Member Function Documentation

int addTorsionTorsion	(	int	particle1,
		int	particle2,
		int	particle3,
		int	particle4,
		int	particle5,
		int	chiralCheckAtomIndex,
		int	gridIndex
	)

Add a torsion-torsion term to the force field.

Parameters

particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the index to the grid to be used

Returns: the index of the torsion-torsion that was added

ForceImpl* createImpl ( ) const

protectedvirtual

When a Context is created, it invokes this method on each Force in the System.

It should create a new ForceImpl object which can be used by the context for calculating forces. The ForceImpl will be deleted automatically when the Context is deleted.

Implements Force.

int getNumTorsionTorsionGrids ( void ) const

inline

Get the number of torsion-torsion grids.

int getNumTorsionTorsions ( void ) const

inline

Get the number of torsion-torsion terms in the potential function.

const std::vector<std::vector<std::vector<double> > >& getTorsionTorsionGrid ( int index ) const

Get the torsion-torsion grid at the specified index.

Parameters

gridIndex the grid index

Returns: grid return grid reference

void getTorsionTorsionParameters	(	int	index,
		int &	particle1,
		int &	particle2,
		int &	particle3,
		int &	particle4,
		int &	particle5,
		int &	chiralCheckAtomIndex,
		int &	gridIndex
	)		const

Get the force field parameters for a torsion-torsion term.

Parameters

index	the index of the torsion-torsion for which to get parameters
particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the grid index

void setTorsionTorsionGrid	(	int	index,
		const std::vector< std::vector< std::vector< double > > > &	grid
	)

Set the torsion-torsion grid at the specified index.

Parameters

index	the index of the torsion-torsion for which to get parameters
grid	either 3 or 6 values may be specified per grid point. If the derivatives are omitted, they are calculated automatically by fitting a 2D spline to the energies. grid[x][y][0] = x value grid[x][y][1] = y value grid[x][y][2] = energy grid[x][y][3] = dEdx value grid[x][y][4] = dEdy value grid[x][y][5] = dEd(xy) value

void setTorsionTorsionParameters	(	int	index,
		int	particle1,
		int	particle2,
		int	particle3,
		int	particle4,
		int	particle5,
		int	chiralCheckAtomIndex,
		int	gridIndex
	)

Set the force field parameters for a torsion-torsion term.

Parameters

index	the index of the torsion-torsion for which to set parameters
particle1	the index of the first particle connected by the torsion-torsion
particle2	the index of the second particle connected by the torsion-torsion
particle3	the index of the third particle connected by the torsion-torsion
particle4	the index of the fourth particle connected by the torsion-torsion
particle5	the index of the fifth particle connected by the torsion-torsion
chiralCheckAtomIndex	the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
gridIndex	the grid index

bool usesPeriodicBoundaryConditions ( ) const

inlinevirtual

Returns whether or not this force makes use of periodic boundary conditions.

Returns: true if nonbondedMethod uses PBC and false otherwise

Reimplemented from Force.

The documentation for this class was generated from the following file:

AmoebaTorsionTorsionForce.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation