Package ffx.numerics.estimator

Class Zwanzig

java.lang.Object

ffx.numerics.estimator.SequentialEstimator

ffx.numerics.estimator.Zwanzig

All Implemented Interfaces:

BootstrappableEstimator, StatisticalEstimator

public class Zwanzig
extends SequentialEstimator
implements BootstrappableEstimator

The Zwanzig class implements exponential averaging/free energy perturbation using the Zwanzig relationship, in either the forwards or backwards direction (not both).

Since:

1.0

Author:

Michael J. Schnieders, Jacob M. Litman

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	Zwanzig.Directionality	Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).

Field Summary

Fields

Modifier and Type	Field	Description
final Zwanzig.Directionality	directionality	Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).

Fields inherited from class ffx.numerics.estimator.SequentialEstimator

eAll, eAllFlat, eAt, eHigh, eLow, lamValues, nTrajectories, snaps, temperatures

Constructor Summary

Constructors

Constructor	Description
Zwanzig(double[] lambdaValues, double[][] energiesLow, double[][] energiesAt, double[][] energiesHigh, double[] temperature, Zwanzig.Directionality directionality)	Estimates a free energy using the Zwanzig relationship.

Method Summary

Modifier and Type	Method	Description
Zwanzig	copyEstimator()	Return a copy of this Estimator.
final void	estimateDG()	Re-calculates free energy and enthalpy without bootstrapping.
final void	estimateDG(boolean randomSamples)	Re-calculates free energy and enthalpy.
double[]	getBinEnergies()	Gets the free energy change per bin/window.
double[]	getBinEnthalpies()	Gets the enthalpy per bin/window.
double[]	getBinUncertainties()	Gets the uncertainty in free energy associated with each bin/window.
double	getFreeEnergy()	Returns the estimated free energy (usually in kcal/mol).
double	getUncertainty()	Returns the uncertainty in the free energy estimate.
int	numberOfBins()	Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute free energy.

Methods inherited from class java.lang.Object

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

Methods inherited from interface ffx.numerics.estimator.BootstrappableEstimator

sumBootstrapEnthalpyUncertainty, sumBootstrapResults, sumBootstrapUncertainty, sumEnthalpyBootstrapResults

Field Details

directionality

public final Zwanzig.Directionality directionality

Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).

Constructor Details

Zwanzig

public Zwanzig(double[] lambdaValues,
 double[][] energiesLow,
 double[][] energiesAt,
 double[][] energiesHigh,
 double[] temperature,
 Zwanzig.Directionality directionality)

Estimates a free energy using the Zwanzig relationship. The temperature array can be of length 1 if all elements are meant to be the same temperature.

The first dimension of the energies arrays corresponds to the lambda values/windows. The second dimension (can be of uneven length) corresponds to potential energies of snapshots sampled from that lambda value, calculated either at that lambda value, the lambda value below, or the lambda value above. The arrays energiesLow[0] and energiesHigh[n-1] is expected to be all NaN.

Parameters:

lambdaValues - Values of lambda dynamics was run at.

energiesLow - Potential energies of trajectory L at lambda L-dL. Ignored for forwards FEP.

energiesAt - Potential energies of trajectory L at lambda L.

energiesHigh - Potential energies of trajectory L at lambda L+dL. Ignored for backwards FEP.

temperature - Temperature each lambda window was run at (single-element indicates identical temperatures).

directionality - Forwards vs. backwards FEP.

Method Details

copyEstimator

public Zwanzig copyEstimator()

Return a copy of this Estimator. Each implementation should specify its own type as the return type. Intended to make parallelization of bootstrapping easy.

Specified by:

copyEstimator in interface BootstrappableEstimator

Returns:

A copy of this Estimator.

estimateDG

public final void estimateDG(boolean randomSamples)

Re-calculates free energy and enthalpy.

Specified by:

estimateDG in interface BootstrappableEstimator

Parameters:

randomSamples - Whether to draw random samples with replacement (one bootstrap trial).

estimateDG

public final void estimateDG()

Re-calculates free energy and enthalpy without bootstrapping.

Specified by:

estimateDG in interface BootstrappableEstimator

getBinEnergies

public double[] getBinEnergies()

Gets the free energy change per bin/window.

Specified by:

getBinEnergies in interface StatisticalEstimator

Returns:

Individual bin/window free energy changes.

getBinUncertainties

public double[] getBinUncertainties()

Gets the uncertainty in free energy associated with each bin/window.

Specified by:

getBinUncertainties in interface StatisticalEstimator

Returns:

Individual bin/window uncertainties.

getFreeEnergy

public double getFreeEnergy()

Returns the estimated free energy (usually in kcal/mol).

Specified by:

getFreeEnergy in interface StatisticalEstimator

Returns:

Free energy estimate.

getUncertainty

public double getUncertainty()

Returns the uncertainty in the free energy estimate.

Specified by:

getUncertainty in interface StatisticalEstimator

Returns:

Uncertainty in the free energy estimate.

numberOfBins

public int numberOfBins()

Returns the number of windows (BAR, etc), bins (WHAM, etc), or other sub-values used to compute free energy.

Specified by:

numberOfBins in interface StatisticalEstimator

Returns:

Total number of sub-values used to compute free energy.

getBinEnthalpies

public double[] getBinEnthalpies()

Gets the enthalpy per bin/window.

Specified by:

getBinEnthalpies in interface StatisticalEstimator

Returns:

Individual bin/window enthalpy.