Package ffx.potential.openmm

Class AmoebaVDWForce

java.lang.Object
ffx.potential.openmm.OpenMMForce
ffx.potential.openmm.AmoebaVDWForce
public class AmoebaVDWForce extends OpenMMForce
The Amoeba vdW Force.

  • Constructor Details

    • AmoebaVDWForce

      public AmoebaVDWForce(OpenMMEnergy openMMEnergy)
      The Amoeba vdW Force constructor.
      Parameters:
      openMMEnergy - The OpenMM Energy instance that contains the vdW parameters.

  • Method Details

    • constructForce

      public static OpenMMForce constructForce(OpenMMEnergy openMMEnergy)
      Convenience method to construct an AMOEBA vdW force.
      Parameters:
      openMMEnergy - The OpenMM Energy instance that contains the vdW information.
      Returns:
      An AMOEBA vdW Force, or null if there are no vdW interactions.

    • updateForce

      public void updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)
      Update the vdW force.
      Parameters:
      atoms - The atoms to update.
      openMMEnergy - The OpenMM Energy instance that contains the vdW parameters.

    • 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, OpenMMIntArray exclusions)
      Set the particle exclusions.
      Parameters:
      i - The particle index.
      exclusions - The exclusions.

    • updateParametersInContext

      public void updateParametersInContext(OpenMMContext openMMContext)
      Update the parameters in the OpenMM Context.
      Parameters:
      openMMContext - The OpenMM Context.