CMAPTorsionForce Class Reference

This class implements an interaction between pairs of dihedral angles. More...

#include <CMAPTorsionForce.h>

Inheritance diagram for CMAPTorsionForce:

Public Member Functions
	CMAPTorsionForce ()
	Create a CMAPTorsionForce.
int	getNumMaps () const
	Get the number of maps that have been defined.
int	getNumTorsions () const
	Get the number of CMAP torsion terms in the potential function.
int	addMap (int size, const std::vector< double > &energy)
	Create a new map that can be used for torsion pairs.
void	getMapParameters (int index, int &size, std::vector< double > &energy) const
	Get the energy values of a map.
void	setMapParameters (int index, int size, const std::vector< double > &energy)
	Set the energy values of a map.
int	addTorsion (int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)
	Add a CMAP torsion term to the force field.
void	getTorsionParameters (int index, int &map, int &a1, int &a2, int &a3, int &a4, int &b1, int &b2, int &b3, int &b4) const
	Get the force field parameters for a CMAP torsion term.
void	setTorsionParameters (int index, int map, int a1, int a2, int a3, int a4, int b1, int b2, int b3, int b4)
	Set the force field parameters for a CMAP torsion term.
Public Member Functions inherited from Force
	Force ()
virtual	~Force ()
int	getForceGroup () const
	Get the force group this Force belongs to.
void	setForceGroup (int group)
	Set the force group this Force belongs to.

Protected Member Functions
ForceImpl *	createImpl () const
	When a Context is created, it invokes this method on each Force in the System.
Protected Member Functions inherited from Force
ForceImpl &	getImplInContext (Context &context)
	Get the ForceImpl corresponding to this Force in a Context.
ContextImpl &	getContextImpl (Context &context)
	Get the ContextImpl corresponding to a Context.

Detailed Description

This class implements an interaction between pairs of dihedral angles.

The interaction energy is defined by an "energy correction map" (CMAP), which is simply a set of tabulated energy values on a regular grid of (phi, psi) angles. Natural cubic spline interpolation is used to compute forces and energies at arbitrary values of the two angles.

To use this class, first create one or more energy correction maps by calling addMap(). For each one, you provide an array of energies at uniformly spaced values of the two angles. Next, add interactions by calling addTorsion(). For each one, you specify the sequence of particles used to calculate each of the two dihedral angles, and the index of the map used to calculate their interaction energy.

Constructor & Destructor Documentation

CMAPTorsionForce

(

)

Create a CMAPTorsionForce.

Member Function Documentation

int addMap	(	int	size,
		const std::vector< double > &	energy
	)

Create a new map that can be used for torsion pairs.

Parameters

size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

Returns

the index of the map that was added

int addTorsion	(	int	map,
		int	a1,
		int	a2,
		int	a3,
		int	a4,
		int	b1,
		int	b2,
		int	b3,
		int	b4
	)

Add a CMAP torsion term to the force field.

Parameters

map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

Returns

the index of the 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.

void getMapParameters	(	int	index,
		int &	size,
		std::vector< double > &	energy
	)		const

Get the energy values of a map.

Parameters

index	the index of the map for which to get energy values
size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

int getNumMaps ( ) const

inline

Get the number of maps that have been defined.

int getNumTorsions ( ) const

inline

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

void getTorsionParameters	(	int	index,
		int &	map,
		int &	a1,
		int &	a2,
		int &	a3,
		int &	a4,
		int &	b1,
		int &	b2,
		int &	b3,
		int &	b4
	)		const

Get the force field parameters for a CMAP torsion term.

Parameters

index	the index of the torsion for which to get parameters
map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

void setMapParameters	(	int	index,
		int	size,
		const std::vector< double > &	energy
	)

Set the energy values of a map.

Parameters

index	the index of the map for which to set energy values
size	the size of the map along each dimension
energy	the energy values for the map. This must be of length size*size. The element energy[i+size*j] contains the energy when the first torsion angle equals i*2*PI/size and the second torsion angle equals j*2*PI/size.

void setTorsionParameters	(	int	index,
		int	map,
		int	a1,
		int	a2,
		int	a3,
		int	a4,
		int	b1,
		int	b2,
		int	b3,
		int	b4
	)

Set the force field parameters for a CMAP torsion term.

Parameters

index	the index of the torsion for which to set parameters
map	the index of the map to use for this term
a1	the index of the first particle forming the first torsion
a2	the index of the second particle forming the first torsion
a3	the index of the third particle forming the first torsion
a4	the index of the fourth particle forming the first torsion
b1	the index of the first particle forming the second torsion
b2	the index of the second particle forming the second torsion
b3	the index of the third particle forming the second torsion
b4	the index of the fourth particle forming the second torsion

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

• CMAPTorsionForce.h