BALL::CharmmNonBonded Class Reference

#include <BALL/MOLMEC/CHARMM/charmmNonBonded.h>

Inheritance diagram for BALL::CharmmNonBonded:

Public Member Functions
Constructors and Destructors
	CharmmNonBonded ()
	CharmmNonBonded (ForceField &force_field)
	CharmmNonBonded (const CharmmNonBonded &charmm_non_bonded)
virtual	~CharmmNonBonded ()
Assignment
const CharmmNonBonded &	operator= (const CharmmNonBonded &charmm_non_bonded)
virtual void	clear ()
Predicates
bool	operator== (const CharmmNonBonded &charmm_non_bonded)
Setup Methods
virtual bool	setup () throw (Exception::TooManyErrors)
Accessors
virtual double	updateEnergy ()
virtual void	updateForces ()
virtual double	getElectrostaticEnergy () const
virtual double	getVdwEnergy () const
virtual double	getSolvationEnergy () const
Neighbourhood and Parameter calculations
virtual MolmecSupport::PairListAlgorithmType	determineMethodOfAtomPairGeneration ()
virtual void	buildVectorOfNonBondedAtomPairs (const std::vector< std::pair< Atom *, Atom * > > &atom_vector) throw (Exception::TooManyErrors)
Public Member Functions inherited from BALL::ForceFieldComponent
	ForceFieldComponent ()
	ForceFieldComponent (ForceField &force_field)
	ForceFieldComponent (const ForceFieldComponent &force_field_component)
virtual	~ForceFieldComponent ()
ForceField *	getForceField () const
void	setForceField (ForceField &force_field)
void	setName (const String &name)
String	getName () const
bool	isEnabled () const
void	setEnabled (bool state)
virtual double	getEnergy () const
virtual void	update () throw (Exception::TooManyErrors)

Protected Attributes
double	electrostatic_energy_
double	vdw_energy_
double	solvation_energy_
Protected Attributes inherited from BALL::ForceFieldComponent
ForceField *	force_field_
double	energy_

Private Attributes
vector< LennardJones::Data >	non_bonded_
vector< bool >	is_torsion_
Size	number_of_1_4_
float	cut_off_
float	cut_off_vdw_
float	cut_on_vdw_
float	cut_off_electrostatic_
float	cut_on_electrostatic_
float	cut_off_solvation_
float	cut_on_solvation_
float	inverse_difference_off_on_vdw_3_
float	inverse_difference_off_on_solvation_3_
float	inverse_difference_off_on_electrostatic_3_
float	scaling_vdw_1_4_
float	scaling_electrostatic_1_4_
bool	use_dist_depend_dielectric_
MolmecSupport::PairListAlgorithmType	algorithm_type_
LennardJones	van_der_waals_parameters_
LennardJones	van_der_waals_parameters_14_
CharmmEEF1	solvation_parameters_
vector< CharmmEEF1::Values >	solvation_
bool	use_solvation_component_

Detailed Description

Charmm NonBonded component. This force field component implements the non-bonded interactions in the CHARMM force field: van-der-Waals interaction, electrostatics, and solvation (in EEF1 only).

Definition at line 45 of file charmmNonBonded.h.

Constructor & Destructor Documentation

BALL::CharmmNonBonded::CharmmNonBonded

(

)

Default constructor.

BALL::CharmmNonBonded::CharmmNonBonded

(

ForceField &

force_field

)

Constructor.

BALL::CharmmNonBonded::CharmmNonBonded

(

const CharmmNonBonded &

charmm_non_bonded

)

Copy constructor

virtual BALL::CharmmNonBonded::~CharmmNonBonded ( )

virtual

Destructor.

Member Function Documentation

virtual void BALL::CharmmNonBonded::buildVectorOfNonBondedAtomPairs ( const std::vector< std::pair< Atom *, Atom * > > &  atom_vector ) throw (Exception::TooManyErrors)

virtual

Build a vector of non-bonded atom pairs with the vdw parameters

virtual void BALL::CharmmNonBonded::clear ( )

virtual

Clear method

virtual MolmecSupport::PairListAlgorithmType BALL::CharmmNonBonded::determineMethodOfAtomPairGeneration ( )

virtual

Computes the most efficient way to calculate the non-bonded atom pairs

virtual double BALL::CharmmNonBonded::getElectrostaticEnergy ( ) const

virtual

Return the electrostatic energy.

virtual double BALL::CharmmNonBonded::getSolvationEnergy ( ) const

virtual

Return the solvation energy.

virtual double BALL::CharmmNonBonded::getVdwEnergy ( ) const

virtual

Return the Van-der-Waals energy.

const CharmmNonBonded& BALL::CharmmNonBonded::operator=

(

const CharmmNonBonded &

charmm_non_bonded

)

Assignment operator

bool BALL::CharmmNonBonded::operator==

(

const CharmmNonBonded &

charmm_non_bonded

)

Equality operator

virtual bool BALL::CharmmNonBonded::setup ( ) throw (Exception::TooManyErrors)

virtual

Setup method.

Reimplemented from BALL::ForceFieldComponent.

virtual double BALL::CharmmNonBonded::updateEnergy ( )

virtual

Calculates and returns the component's energy.

Reimplemented from BALL::ForceFieldComponent.

virtual void BALL::CharmmNonBonded::updateForces ( )

virtual

Calculates and returns the component's forces.

Reimplemented from BALL::ForceFieldComponent.

Member Data Documentation

MolmecSupport::PairListAlgorithmType BALL::CharmmNonBonded::algorithm_type_

private

Definition at line 259 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_off_

private

Definition at line 204 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_off_electrostatic_

private

Definition at line 216 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_off_solvation_

private

Definition at line 224 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_off_vdw_

private

Definition at line 208 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_on_electrostatic_

private

Definition at line 220 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_on_solvation_

private

Definition at line 228 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::cut_on_vdw_

private

Definition at line 212 of file charmmNonBonded.h.

double BALL::CharmmNonBonded::electrostatic_energy_

protected

Definition at line 172 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::inverse_difference_off_on_electrostatic_3_

private

Definition at line 240 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::inverse_difference_off_on_solvation_3_

private

Definition at line 236 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::inverse_difference_off_on_vdw_3_

private

Definition at line 232 of file charmmNonBonded.h.

vector<bool> BALL::CharmmNonBonded::is_torsion_

private

Definition at line 196 of file charmmNonBonded.h.

vector<LennardJones::Data> BALL::CharmmNonBonded::non_bonded_

private

Definition at line 191 of file charmmNonBonded.h.

Size BALL::CharmmNonBonded::number_of_1_4_

private

Definition at line 200 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::scaling_electrostatic_1_4_

private

Definition at line 248 of file charmmNonBonded.h.

float BALL::CharmmNonBonded::scaling_vdw_1_4_

private

Definition at line 244 of file charmmNonBonded.h.

vector<CharmmEEF1::Values> BALL::CharmmNonBonded::solvation_

private

Definition at line 267 of file charmmNonBonded.h.

double BALL::CharmmNonBonded::solvation_energy_

protected

Definition at line 180 of file charmmNonBonded.h.

CharmmEEF1 BALL::CharmmNonBonded::solvation_parameters_

private

Definition at line 265 of file charmmNonBonded.h.

bool BALL::CharmmNonBonded::use_dist_depend_dielectric_

private

Definition at line 253 of file charmmNonBonded.h.

bool BALL::CharmmNonBonded::use_solvation_component_

private

Definition at line 269 of file charmmNonBonded.h.

LennardJones BALL::CharmmNonBonded::van_der_waals_parameters_

private

Definition at line 261 of file charmmNonBonded.h.

LennardJones BALL::CharmmNonBonded::van_der_waals_parameters_14_

private

Definition at line 263 of file charmmNonBonded.h.

double BALL::CharmmNonBonded::vdw_energy_

protected

Definition at line 176 of file charmmNonBonded.h.