Package ffx.openmm

Class OutOfPlaneSite

java.lang.Object

ffx.openmm.VirtualSite

ffx.openmm.OutOfPlaneSite

public class OutOfPlaneSite
extends VirtualSite

This is a VirtualSite that computes the particle location based on three other particles' locations. If r₁ is the location of particle 1, r₁₂ is the vector from particle 1 to particle 2, and r₁₃ is the vector from particle 1 to particle 3, then the virtual site location is given by

r₁ + w₁₂r₁₂ + w₁₃r₁₃ + w_cross(r₁₂ x r₁₃)

The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles. Note that while w₁₂ and w₁₃ are unitless, w_cross has units of inverse distance.

Field Summary

Fields inherited from class ffx.openmm.VirtualSite

pointer

Constructor Summary

Constructors

Constructor	Description
OutOfPlaneSite(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross)	Create an OutOfPlaneSite.

Method Summary

Modifier and Type	Method	Description
void	destroy()	Destroy the virtual site.
double	getWeight12()	Get the weight for the vector from particle1 to particle2.
double	getWeight13()	Get the weight for the vector from particle1 to particle3.
double	getWeightCross()	Get the weight for the cross product of the two vectors.

Methods inherited from class ffx.openmm.VirtualSite

getNumParticles, getParticle, getPointer

Methods inherited from class java.lang.Object

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

Constructor Details

OutOfPlaneSite

public OutOfPlaneSite(int particle1,
 int particle2,
 int particle3,
 double weight12,
 double weight13,
 double weightCross)

Create an OutOfPlaneSite.

Parameters:

particle1 - The index of the first particle.

particle2 - The index of the second particle.

particle3 - The index of the third particle.

weight12 - The weight for the vector from particle1 to particle2.

weight13 - The weight for the vector from particle1 to particle3.

weightCross - The weight for the cross product of the two vectors.

Method Details

destroy

public void destroy()

Destroy the virtual site.

Specified by:

destroy in class VirtualSite

getWeight12

public double getWeight12()

Get the weight for the vector from particle1 to particle2.

Returns:

The weight12 parameter.

getWeight13

public double getWeight13()

Get the weight for the vector from particle1 to particle3.

Returns:

The weight13 parameter.

getWeightCross

public double getWeightCross()

Get the weight for the cross product of the two vectors.

Returns:

The weightCross parameter.