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Last data update: 2014.03.03

R: Thermodynamic integration plot

TIcurve

R Documentation

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).

Author(s)

Christian Margreitter

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 )

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MDplot)
Loading required package: MASS
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: gtools
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MDplot/TIcurve.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TIcurve
> ### Title: Thermodynamic integration plot
> ### Aliases: TIcurve
> ### Keywords: Thermodynamic integration
> 
> ### ** Examples
> 
> # see "extdata/TIcurve_example.txt.gz" for format information
> TIcurve( load_TIcurve( system.file( "extdata/TIcurve_example.txt.gz",
+                                     package = "MDplot" ) ) )
$lambdapoints
$lambdapoints[[1]]
         V1          V2        V3       V4
 [1,] 0.000  70.6728992 0.9779597 15.66871
 [2,] 0.050  72.1676402 1.2490862 16.23625
 [3,] 0.100  69.6754518 0.6666403 16.98315
 [4,] 0.150  68.4934444 0.8949250 17.84841
 [5,] 0.200  64.2735409 0.8117664 17.83949
 [6,] 0.250  67.2477093 0.9803661 18.97459
 [7,] 0.300  61.4080938 0.8264187 18.62204
 [8,] 0.350  59.7371239 0.7567702 20.81682
 [9,] 0.400  57.7425588 0.7203468 21.33566
[10,] 0.450  55.1339043 0.5494124 22.62585
[11,] 0.500  52.8220525 0.7202825 25.33042
[12,] 0.550  48.0230784 0.6059083 27.92609
[13,] 0.600  38.2991351 1.0791823 44.54838
[14,] 0.650  -0.9665448 3.0670393 65.78960
[15,] 0.700 -12.3715351 0.7424810 39.65973
[16,] 0.750  12.1538035 0.4968396 22.25272
[17,] 0.800  38.4030003 0.6138009 17.66457
[18,] 0.825  50.3454393 0.4347878 16.41228
[19,] 0.850  60.6411194 0.4086155 17.07396
[20,] 0.875  70.6331438 0.4434030 17.19864
[21,] 0.900  78.8147193 0.3073863 19.45543
[22,] 0.950  97.2657422 0.2690783 22.74265
[23,] 1.000 120.4053780 1.2807035 34.37515


$integrationresults
        deltaG error
forward   54.3   0.8

$hysteresis
[1] NA

> 
> # 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 )
$lambdapoints
$lambdapoints[[1]]
       V1         V2         V3
 [1,] 0.0   6.200384 0.24245318
 [2,] 0.1  -1.262444 0.24289737
 [3,] 0.2 -10.467038 0.86256397
 [4,] 0.3 -14.041000 0.57389429
 [5,] 0.4 -19.394170 2.09316459
 [6,] 0.5 -21.851126 1.51855182
 [7,] 0.6 -12.709041 1.34143256
 [8,] 0.7   0.426108 1.02640371
 [9,] 0.8  13.878155 0.60923413
[10,] 0.9  17.870409 0.21193239
[11,] 1.0  16.516691 0.05706165

$lambdapoints[[2]]
       V1         V2         V3
 [1,] 0.0   6.149830 0.05927549
 [2,] 0.1  -1.873073 0.22215602
 [3,] 0.2  -9.806893 0.40698736
 [4,] 0.3 -14.372397 1.20742891
 [5,] 0.4 -20.151894 1.51859105
 [6,] 0.5 -23.258170 1.67165159
 [7,] 0.6 -14.145401 1.53494884
 [8,] 0.7   2.473518 0.55384735
 [9,] 0.8  13.567718 0.54018345
[10,] 0.9  17.759051 0.31150726
[11,] 1.0  16.590724 0.31085689


$integrationresults
         deltaG error
forward    -3.6   0.9
backward   -3.8   0.8

$hysteresis
integral.V1 
        0.2 

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>