Package ffx.potential.nonbonded.implicit

Class ChandlerCavitation

java.lang.Object

ffx.potential.nonbonded.implicit.ChandlerCavitation

public class ChandlerCavitation
extends Object

The ChandlerCavitation class smoothly switches between a volume based dependence for small solutes to a surface area dependence for large solutes.

Since:

1.0

Author:

Michael J. Schnieders

Constructor Summary

Constructors

Constructor	Description
ChandlerCavitation(Atom[] atoms, ConnollyRegion connollyRegion, ForceField forceField)
ChandlerCavitation(Atom[] atoms, GaussVol gaussVol, ForceField forceField)

Method Summary

Modifier and Type	Method	Description
double	energyAndGradient(double[][] positions, AtomicDoubleArray3D gradient)	Compute molecular volume and surface area.
double	energyAndGradientConnolly(AtomicDoubleArray3D gradient)	Compute the cavitation energy.
double	energyAndGradientGausVol(double[][] positions, AtomicDoubleArray3D gradient)	Compute molecular volume and surface area.
ConnollyRegion	getConnollyRegion()
double	getCrossOver()
double	getEffectiveRadius()
double	getEnergy()
GaussVol	getGaussVol()
double	getSolventPressure()
double	getSurfaceArea()	Return Surface Area (A^2).
double	getSurfaceAreaEnergy()	Return Surface Area based cavitation energy.
double	getSurfaceTension()
double	getVolume()	Return Volume (A^3).
double	getVolumeEnergy()	Return Volume based cavitation energy.
void	setCrossOver(double crossOver)
void	setSolventPressure(double solventPressure)
void	setSurfaceTension(double surfaceTension)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ChandlerCavitation

public ChandlerCavitation(Atom[] atoms,
 GaussVol gaussVol,
 ForceField forceField)

ChandlerCavitation

public ChandlerCavitation(Atom[] atoms,
 ConnollyRegion connollyRegion,
 ForceField forceField)

Method Details

energyAndGradient

public double energyAndGradient(double[][] positions,
 AtomicDoubleArray3D gradient)

Compute molecular volume and surface area.

Parameters:

positions - Atomic positions to use.

gradient - Atomic coordinate gradient.

Returns:

The cavitation energy.

energyAndGradientConnolly

public double energyAndGradientConnolly(AtomicDoubleArray3D gradient)

Compute the cavitation energy.

Parameters:

gradient - Add the gradient to this AtomicDoubleArray3D.

Returns:

Returns the cavitation energy.

energyAndGradientGausVol

public double energyAndGradientGausVol(double[][] positions,
 AtomicDoubleArray3D gradient)

Compute molecular volume and surface area.

Parameters:

positions - Atomic positions to use.

gradient - Atomic coordinate gradient.

Returns:

The cavitation energy.

getConnollyRegion

public ConnollyRegion getConnollyRegion()

getCrossOver

public double getCrossOver()

setCrossOver

public void setCrossOver(double crossOver)

getEffectiveRadius

public double getEffectiveRadius()

getEnergy

public double getEnergy()

getGaussVol

public GaussVol getGaussVol()

getSolventPressure

public double getSolventPressure()

setSolventPressure

public void setSolventPressure(double solventPressure)

getSurfaceArea

public double getSurfaceArea()

Return Surface Area (A^2).

Returns:

Surface Area (A^2).

getSurfaceAreaEnergy

public double getSurfaceAreaEnergy()

Return Surface Area based cavitation energy.

Returns:

Surface Area based cavitation energy.

getSurfaceTension

public double getSurfaceTension()

setSurfaceTension

public void setSurfaceTension(double surfaceTension)

getVolume

public double getVolume()

Return Volume (A^3).

Returns:

Volume (A^3).

getVolumeEnergy

public double getVolumeEnergy()

Return Volume based cavitation energy.

Returns:

Volume based cavitation energy.