MDplot (version 1.0.1)

TIcurve: Thermodynamic integration plot

Description

Plot the thermodynamic integration(s) (TIs) specified in the input files. Files have to have at least three columns (lambda point, free energy and error) in order to be valid. In addition, the delta free energiy (to a precision dependent on the error) are calculated. In case, two data input series are provided, the hysteresis is calculated.

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.

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 integration and error 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).

Value

Returns a list with the the following information:

• integrationresults A matrix containing one row of "deltaG" and "error" columns from the integration for every data input series.

• hysteresis If two (i.e. forward and backward) data input series are provided, the resulting hysteresis is reported (and set to be NA otherwise).

Examples

# GROMOS (forward integration)
TIcurve( load_TIcurve( system.file( "extdata/TIcurve_example.txt.gz",
                                    package = "MDplot" ) ) )

# GROMOS (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 )