Package ffx.openmm.amoeba

Class VdwForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.amoeba.VdwForce

Direct Known Subclasses:

AmoebaVdwForce

public class VdwForce
extends Force

Amoeba van der Waals Force.

Field Summary

Fields inherited from class ffx.openmm.Force

pointer

Constructor Summary

Constructors

Constructor	Description
VdwForce()	The Amoeba vdW Force constructor.

Method Summary

Modifier and Type	Method	Description
void	addParticle_1(int ired, int type, double reductionFactor, int isAlchemical, double scaleFactor)	Add a particle to the vdW Force.
int	addParticleType(double rad, double eps)	Add a particle type to the vdW Force.
void	addTypePair(int type1, int type2, double rad, double eps)	Add a type pair to the vdW Force.
void	destroy()	Destroy the vdW Force.
void	setAlchemicalMethod(int method)	Set the alchemical method.
void	setCutoffDistance(double cutoff)	Set the cutoff distance.
void	setNonbondedMethod(int method)	Set the non-bonded method.
void	setParticleExclusions(int i, IntArray exclusions)	Set the particle exclusions.
void	setParticleParameters(int index, int ired, double rad, double eps, double reductionFactor, int isAlchemical, int type, double scaleFactor)	Set the particle parameters.
void	setSoftcoreAlpha(double vdWSoftcoreAlpha)	Set the softcore power.
void	setSoftcorePower(int vdwSoftcorePower)	Set the softcore power.
void	setUseDispersionCorrection(int value)	Set the vdW force to use a long-range dispersion correction.
void	updateParametersInContext(Context context)	Update the parameters in the OpenMM Context.

Methods inherited from class ffx.openmm.Force

getForceGroup, getForceIndex, getName, getPointer, setForceGroup, setForceIndex, setName, usesPeriodicBoundaryConditions

Methods inherited from class java.lang.Object

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

Constructor Details

VdwForce

public VdwForce()

The Amoeba vdW Force constructor.

Method Details

addParticleType

public int addParticleType(double rad,
 double eps)

Add a particle type to the vdW Force.

Parameters:

rad - The radius.

eps - The well depth.

Returns:

The type.

addTypePair

public void addTypePair(int type1,
 int type2,
 double rad,
 double eps)

Add a type pair to the vdW Force.

Parameters:

type1 - The first type.

type2 - The second type.

rad - The radius.

eps - The well depth.

addParticle_1

public void addParticle_1(int ired,
 int type,
 double reductionFactor,
 int isAlchemical,
 double scaleFactor)

Add a particle to the vdW Force.

Parameters:

ired - The particle ired.

type - The particle type.

reductionFactor - The reduction factor.

isAlchemical - The alchemical flag.

scaleFactor - The scale factor.

setParticleParameters

public void setParticleParameters(int index,
 int ired,
 double rad,
 double eps,
 double reductionFactor,
 int isAlchemical,
 int type,
 double scaleFactor)

Set the particle parameters.

Parameters:

index - The particle index.

ired - The particle reduction index.

rad - The radius.

eps - The well depth.

reductionFactor - The reduction factor.

isAlchemical - The alchemical flag.

type - The type.

scaleFactor - The scale factor.

setCutoffDistance

public void setCutoffDistance(double cutoff)

Set the cutoff distance.

Parameters:

cutoff - The cutoff distance.

setUseDispersionCorrection

public void setUseDispersionCorrection(int value)

Set the vdW force to use a long-range dispersion correction.

Parameters:

value - The flag.

setNonbondedMethod

public void setNonbondedMethod(int method)

Set the non-bonded method.

Parameters:

method - The non-bonded method.

setAlchemicalMethod

public void setAlchemicalMethod(int method)

Set the alchemical method.

Parameters:

method - The alchemical method.

setSoftcoreAlpha

public void setSoftcoreAlpha(double vdWSoftcoreAlpha)

Set the softcore power.

Parameters:

vdWSoftcoreAlpha - The softcore power.

setSoftcorePower

public void setSoftcorePower(int vdwSoftcorePower)

Set the softcore power.

Parameters:

vdwSoftcorePower - The softcore power.

setParticleExclusions

public void setParticleExclusions(int i,
 IntArray exclusions)

Set the particle exclusions.

Parameters:

i - The particle index.

exclusions - The exclusions.

updateParametersInContext

public void updateParametersInContext(Context context)

Update the parameters in the OpenMM Context.

Parameters:

context - The OpenMM Context.

destroy

public void destroy()

Destroy the vdW Force.