MDplot (version 0.3.1)

TIcurve: Thermodynamic integration plot

Description

Plot the thermodynamic integration(s) (TI) specified in the input files. Files have to have three columns (lambda point, free energy and error) in order to be valid. In addtion, the delta free energies are calculated (to a precision dependent on the error size) and the hysteresis is calculated in case a forward and backward simulation have been performed.

Usage

TIcurve( lambdas, invertedBackwards = FALSE, energyUnit = "kJ/mol", printValues = TRUE, printErrors = TRUE, errorBarThreshold = 0, barePlot = FALSE, ... )

Arguments

lambdas

List of matrices (automatically generated by load_TIcurve()) holding the thermodynamic integration information. For the file format, see the description.

invertedBackwards

In case a forward and backward TI have been performed and the lambda points are enumerated reversely (i.e. 0.3 of one TI is equivalent to 0.7 of the other), this flag can be set to be TRUE in order to automatically mirror the values appropriately.

energyUnit

Defines the energy unit used for the plot.

printValues

Boolean, indicating whether the computed values are to be plotted.

printErrors

Boolean, indicating whether error bars are to be plotted.

errorBarThreshold

If the error at a given lambda point is below this theshold, it is not plotted.

barePlot

Boolean, indicating whether the plot is to be made without any additional information.

...

Additional arguments (ellipsis).

Examples

# see "extdata/TIcurve_example.txt.gz" for format information
TIcurve( load_TIcurve( system.file( "extdata/TIcurve_example.txt.gz",
                                    package = "MDplot" ) ) )

# forward and backward integration
TIcurve( load_TIcurve( c( system.file( "extdata/TIcurve_fb_forward_example.txt.gz",
                                       package = "MDplot" ),
                          system.file( "extdata/TIcurve_fb_backward_example.txt.gz",
                          package = "MDplot" ) ) ),
         invertedBackwards = TRUE )