Package ffx.openmm

Class NonbondedForce

java.lang.Object

ffx.openmm.Force

ffx.openmm.NonbondedForce

Direct Known Subclasses:

FixedChargeNonbondedForce

public class NonbondedForce
extends Force

Nonbonded Force.

Field Summary

Fields inherited from class ffx.openmm.Force

pointer

Constructor Summary

Constructors

Constructor	Description
NonbondedForce()

Method Summary

Modifier and Type	Method	Description
void	addParticle(double charge, double sigma, double eps)	Add a particle.
void	createExceptionsFromBonds(BondArray bondArray, double coulomb14Scale, double lj14Scale)	Create exceptions from bonds.
void	destroy()
void	getExceptionParameters(int index, com.sun.jna.ptr.IntByReference particle1, com.sun.jna.ptr.IntByReference particle2, com.sun.jna.ptr.DoubleByReference chargeProd, com.sun.jna.ptr.DoubleByReference sigma, com.sun.jna.ptr.DoubleByReference eps)	Get the exception parameters.
int	getNumExceptions()	Get the number of exceptions.
void	getParticleParameters(int index, com.sun.jna.ptr.DoubleByReference charge, com.sun.jna.ptr.DoubleByReference sigma, com.sun.jna.ptr.DoubleByReference eps)	Get the particle parameters.
void	setCutoffDistance(double cutoffDistance)	Set the cutoff distance.
void	setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double eps)	Set the exception parameters.
void	setNonbondedMethod(int method)	Set the nonbonded method.
void	setParticleParameters(int index, double charge, double sigma, double eps)	Set the particle parameters.
void	setPMEParameters(double aEwald, int nx, int ny, int nz)	Set the PME parameters.
void	setSwitchingDistance(double switchingDistance)	Set the switching distance.
void	setUseDispersionCorrection(int useDispersionCorrection)	Set if a dispersion correction will be used.
void	setUseSwitchingFunction(int useSwitchingFunction)	Set if a switching function will be used.
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

NonbondedForce

public NonbondedForce()

Method Details

addParticle

public void addParticle(double charge,
 double sigma,
 double eps)

Add a particle.

Parameters:

charge - The atomic charge.

sigma - The vdW sigma.

eps - The vdW eps.

setParticleParameters

public void setParticleParameters(int index,
 double charge,
 double sigma,
 double eps)

Set the particle parameters.

Parameters:

index - The particle index.

charge - The atomic charge.

sigma - The vdW sigma.

eps - The vdW eps.

getParticleParameters

public void getParticleParameters(int index,
 com.sun.jna.ptr.DoubleByReference charge,
 com.sun.jna.ptr.DoubleByReference sigma,
 com.sun.jna.ptr.DoubleByReference eps)

Get the particle parameters.

Parameters:

index - The particle index.

charge - The atomic charge.

sigma - The vdW sigma.

eps - The vdW eps.

createExceptionsFromBonds

public void createExceptionsFromBonds(BondArray bondArray,
 double coulomb14Scale,
 double lj14Scale)

Create exceptions from bonds.

Parameters:

bondArray - The bond array.

coulomb14Scale - The coulomb 1-4 scale.

lj14Scale - The LJ 1-4 scale.

getExceptionParameters

public void getExceptionParameters(int index,
 com.sun.jna.ptr.IntByReference particle1,
 com.sun.jna.ptr.IntByReference particle2,
 com.sun.jna.ptr.DoubleByReference chargeProd,
 com.sun.jna.ptr.DoubleByReference sigma,
 com.sun.jna.ptr.DoubleByReference eps)

Get the exception parameters.

Parameters:

index - The exception index.

particle1 - The first particle.

particle2 - The second particle.

chargeProd - The charge product.

sigma - The sigma vdW parameter.

eps - The eps vdW parameter.

setExceptionParameters

public void setExceptionParameters(int index,
 int particle1,
 int particle2,
 double chargeProd,
 double sigma,
 double eps)

Set the exception parameters.

Parameters:

index - The exception index.

particle1 - The first particle.

particle2 - The second particle.

chargeProd - The charge product.

sigma - The sigma vdW parameter.

eps - The eps vdW parameter.

setNonbondedMethod

public void setNonbondedMethod(int method)

Set the nonbonded method.

Parameters:

method - The nonbonded method.

setPMEParameters

public void setPMEParameters(double aEwald,
 int nx,
 int ny,
 int nz)

Set the PME parameters.

Parameters:

aEwald - The Ewald alpha.

nx - The PME grid size in x.

ny - The PME grid size in y.

nz - The PME grid size in z.

setCutoffDistance

public void setCutoffDistance(double cutoffDistance)

Set the cutoff distance.

Parameters:

cutoffDistance - The cutoff distance.

setUseSwitchingFunction

public void setUseSwitchingFunction(int useSwitchingFunction)

Set if a switching function will be used.

Parameters:

useSwitchingFunction - The switching distance flag.

setSwitchingDistance

public void setSwitchingDistance(double switchingDistance)

Set the switching distance.

Parameters:

switchingDistance - The switching distance.

setUseDispersionCorrection

public void setUseDispersionCorrection(int useDispersionCorrection)

Set if a dispersion correction will be used.

Parameters:

useDispersionCorrection - The dispersion correction flag.

getNumExceptions

public int getNumExceptions()

Get the number of exceptions.

Returns:

The number of exceptions.

updateParametersInContext

public void updateParametersInContext(Context context)

Update the parameters in the OpenMM Context.

Parameters:

context - The OpenMM Context.

destroy

public void destroy()