Package ffx.openmm.amoeba

Class WcaDispersionForce

java.lang.Object
ffx.openmm.Force
ffx.openmm.amoeba.WcaDispersionForce
Direct Known Subclasses:
AmoebaWcaDispersionForce
public class WcaDispersionForce extends Force
This class implements a nonbonded interaction between pairs of particles typically used along with AmoebaGeneralizedKirkwoodForce as part of an implicit solvent model.

To use it, create an AmoebaWcaDispersionForce object then call addParticle() once for each particle. After a particle has been added, you can modify its force field parameters by calling setParticleParameters(). This will have no effect on Contexts that already exist unless you call updateParametersInContext().

  • Constructor Details

    • WcaDispersionForce

      public WcaDispersionForce()
      Create an AmoebaWcaDispersionForce.

  • Method Details

    • addParticle

      public int addParticle(double radius, double epsilon)
      Add a particle to the force field.
      Parameters:
      radius - radius
      epsilon - epsilon
      Returns:
      index of added particle

    • destroy

      public void destroy()
      Destroy the force.
      Specified by:
      destroy in class Force

    • getAwater

      public double getAwater()
      Get the water density parameter.
      Returns:
      The water density parameter.

    • getDispoff

      public double getDispoff()
      Get the dispersion offset.
      Returns:
      The dispersion offset.

    • getEpsh

      public double getEpsh()
      Get the water hydrogen epsilon parameter.
      Returns:
      The water hydrogen epsilon parameter.

    • getEpso

      public double getEpso()
      Get the water oxygen epsilon parameter.
      Returns:
      The water oxygen epsilon parameter.

    • getNumParticles

      public int getNumParticles()
      Get the number of particles

    • getParticleParameters

      public void getParticleParameters(int particleIndex, com.sun.jna.ptr.DoubleByReference radius, com.sun.jna.ptr.DoubleByReference epsilon)
      Get the force field parameters for a WCA dispersion particle.
      Parameters:
      particleIndex - the particle index
      radius - radius
      epsilon - epsilon

    • getRminh

      public double getRminh()
      Get the water hydrogen radius parameter.
      Returns:
      The water hydrogen radius parameter.

    • getRmino

      public double getRmino()
      Get the water oxygen radius parameter.
      Returns:
      The water oxygen radius parameter.

    • getShctd

      public double getShctd()
      Get the overlap factor.
      Returns:
      The overlap factor.

    • getSlevy

      public double getSlevy()
      Get the Levy parameter.
      Returns:
      The Levy parameter.

    • setAwater

      public void setAwater(double awater)
      Set the water density parameter.
      Parameters:
      awater - The water density parameter.

    • setDispoff

      public void setDispoff(double dispoff)
      Set the dispersion offset.
      Parameters:
      dispoff - The dispersion offset.

    • setEpsh

      public void setEpsh(double epsh)
      Set the water hydrogen epsilon parameter.
      Parameters:
      epsh - The water hydrogen epsilon parameter.

    • setEpso

      public void setEpso(double epso)
      Set the water oxygen epsilon parameter.
      Parameters:
      epso - The water oxygen epsilon parameter.

    • setParticleParameters

      public void setParticleParameters(int particleIndex, double radius, double epsilon)
      Set the force field parameters for a WCA dispersion particle.
      Parameters:
      particleIndex - the particle index
      radius - radius
      epsilon - epsilon

    • setRminh

      public void setRminh(double rminh)
      Set the water hydrogen radius parameter.
      Parameters:
      rminh - The water hydrogen radius parameter.

    • setRmino

      public void setRmino(double rmino)
      Set the water oxygen radius parameter.
      Parameters:
      rmino - The water oxygen radius parameter.

    • setShctd

      public void setShctd(double shctd)
      Set the overlap factor.
      Parameters:
      shctd - The overlap factor.

    • setSlevy

      public void setSlevy(double slevy)
      Set the Levy parameter.
      Parameters:
      slevy - The Levy parameter.

    • updateParametersInContext

      public void updateParametersInContext(Context context)
      Update the per-particle parameters in a Context to match those stored in this Force object. This method provides an efficient method to update certain parameters in an existing Context without needing to reinitialize it. Simply call setParticleParameters() to modify this object's parameters, then call updateParametersInContext() to copy them over to the Context.

      The only information this method updates is the values of per-particle parameters. All other aspects of the Force are unaffected and can only be changed by reinitializing the Context.

    • usesPeriodicBoundaryConditions

      public boolean usesPeriodicBoundaryConditions()
      Returns whether or not this force makes use of periodic boundary conditions.
      Overrides:
      usesPeriodicBoundaryConditions in class Force
      Returns:
      true if nonbondedMethod uses PBC and false otherwise