Package ffx.numerics.estimator

Class FreeEnergyDifferenceReporter

java.lang.Object
ffx.numerics.estimator.FreeEnergyDifferenceReporter
public class FreeEnergyDifferenceReporter extends Object
The FreeEnergyDifferenceReporter class reports free energy differences using the Bennett Acceptance Ratio (BAR) method.
Since:
1.0
Author:
Michael J. Schnieders

  • Constructor Details

    • FreeEnergyDifferenceReporter

      public FreeEnergyDifferenceReporter(int nStates, double[] lambdaValues, double[] temperature, double eps, int nIterations, double[][] energiesLow, double[][] energiesAt, double[][] energiesHigh, double[][] volume)
      Report Free Energy Differences based on a series of states.
      Parameters:
      nStates - The number of states.
      lambdaValues - The lambda value for each state.
      temperature - The temperature for each state.
      eps - The BAR convergence criteria.
      nIterations - The BAR maximum number of iterations.
      energiesLow - The energy for each snapshot from state L evaluated at L - dL.
      energiesAt - The energy for each snapshot from state L evaluated at L.
      energiesHigh - The energy for each snapshot from state L evaluated at L + dL.
      volume - The volume for each snapshot from state L.

  • Method Details

    • report

      public void report()
      Report the free energy differences.

    • getForwardTotalFEDifference

      public double getForwardTotalFEDifference()
      Free energy difference from forward FEP.
      Returns:
      the forward total free energy difference.

    • getForwardTotalEnthalpyChange

      public double getForwardTotalEnthalpyChange()
      Enthalpy difference from forward FEP.
      Returns:
      the forward total enthalpy change.

    • getForwardTotalEntropyChange

      public double getForwardTotalEntropyChange()
      Entropy difference from forward FEP.
      Returns:
      the forward total entropy change.

    • getBackwardTotalFEDifference

      public double getBackwardTotalFEDifference()
      Free energy difference from backward FEP.
      Returns:
      the backward total free energy difference.

    • getBackwardTotalEnthalpyChange

      public double getBackwardTotalEnthalpyChange()
      Enthalpy difference from backward FEP.
      Returns:
      the backward total enthalpy change.

    • getBackwardTotalEntropyChange

      public double getBackwardTotalEntropyChange()
      Entropy difference from backward FEP.
      Returns:
      the backward total entropy change.

    • getBarIterTotalFEDiff

      public double getBarIterTotalFEDiff()
      Free energy difference from BAR.
      Returns:
      the BAR iteration total free energy difference.

    • getBarBSTotalFEDiff

      public double getBarBSTotalFEDiff()
      Free energy difference from BAR using boot-strapping.
      Returns:
      the BAR boot-strap total free energy difference.

    • getBarBSTotalEnthalpyChange

      public double getBarBSTotalEnthalpyChange()
      Enthalpy difference from BAR.
      Returns:
      the BAR boot-strap total enthalpy change.

    • getBarBSTotalEntropyChange

      public double getBarBSTotalEntropyChange()
      Entropy difference from BAR.
      Returns:
      the BAR boot-strap total entropy change.