TIcurve: Thermodynamic integration plot

In MDplot: Visualising Molecular Dynamics Analyses

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:

• lambdapoints A list containing a (at least) nx3-matrix for every data input series.

• 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).

Author(s)

Christian Margreitter

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 )

Example output

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
$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

$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 

MDplot documentation built on May 2, 2019, 7:02 a.m.