Package ffx.potential.nonbonded.pme

Class AlchemicalParameters

java.lang.Object
ffx.potential.nonbonded.pme.AlchemicalParameters
public class AlchemicalParameters extends Object

  • Field Details

    • mode

      public final AlchemicalParameters.AlchemicalMode mode
      The alchemical mode to use.

    • permLambdaAlpha

      public double permLambdaAlpha
      Constant α in: r' = sqrt(r^2 + α*(1 - L)^2)

    • permLambdaExponent

      public double permLambdaExponent
      Power on L in front of the pairwise multipole potential.

    • permLambdaStart

      public double permLambdaStart
      Begin turning on permanent multipoles at Lambda = 0.4;

    • permLambdaEnd

      public double permLambdaEnd
      Finish turning on permanent multipoles at Lambda = 1.0;

    • polLambdaStart

      public double polLambdaStart
      Start turning on polarization later in the Lambda path to prevent SCF convergence problems when atoms nearly overlap.

    • polLambdaEnd

      public double polLambdaEnd

    • polLambdaExponent

      public double polLambdaExponent
      Power on L in front of the polarization energy.

    • doLigandVaporElec

      public boolean doLigandVaporElec
      Intramolecular electrostatics for the ligand in vapor is included by default.

    • doLigandGKElec

      public boolean doLigandGKElec
      Intramolecular electrostatics for the ligand in done in GK implicit solvent.

    • doNoLigandCondensedSCF

      public boolean doNoLigandCondensedSCF
      Condensed phase SCF without the ligand present is included by default. For DualTopologyEnergy calculations it can be turned off.

    • lAlpha

      public double lAlpha
      lAlpha = α*(1 - L)^2

    • dlAlpha

      public double dlAlpha

    • d2lAlpha

      public double d2lAlpha

    • dEdLSign

      public double dEdLSign

    • lPowPerm

      public double lPowPerm
      lPowPerm = L^permanentLambdaExponent

    • dlPowPerm

      public double dlPowPerm

    • d2lPowPerm

      public double d2lPowPerm

    • doPermanentRealSpace

      public boolean doPermanentRealSpace

    • permanentScale

      public double permanentScale

    • lPowPol

      public double lPowPol
      lPowPol = L^polarizationLambdaExponent

    • dlPowPol

      public double dlPowPol

    • d2lPowPol

      public double d2lPowPol

    • doPolarization

      public boolean doPolarization

    • polarizationScale

      public double polarizationScale
      When computing the polarization energy at L there are 3 pieces.

      1.) Upol(1) = The polarization energy computed normally (ie. system with ligand).

      2.) Uenv = The polarization energy of the system without the ligand.

      3.) Uligand = The polarization energy of the ligand by itself.

      Upol(L) = L*Upol(1) + (1-L)*(Uenv + Uligand)

      Set polarizationScale to L for part 1. Set polarizationScale to (1-L) for parts 2 and 3.

    • polLambda

      public double polLambda
      The polarization Lambda value goes from 0.0 .. 1.0 as the global lambda value varies between polLambdaStart .. polLambadEnd.

    • permLambda

      public double permLambda
      The permanent Lambda value goes from 0.0 .. 1.0 as the global lambda value varies between permLambdaStart .. permLambdaEnd.

    • vaporCrystal

      public Crystal vaporCrystal
      Boundary conditions for the vapor end of the alchemical path.

    • vaporLists

      public int[][][] vaporLists

    • vacuumRanges

      public Range[] vacuumRanges

    • vaporPermanentSchedule

      public IntegerSchedule vaporPermanentSchedule

    • vaporEwaldSchedule

      public IntegerSchedule vaporEwaldSchedule

  • Constructor Details

    • AlchemicalParameters

      public AlchemicalParameters(ForceField forceField, boolean lambdaTerm, boolean nnTerm, Polarization polarization)

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • update

      public void update(double lambda)