Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 5 6 7 8 |
lambdas |
List of matrices (automatically generated by |
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 |
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). |
Returns a list with the the following information:
lambdapoints
A list containing a (at least) n
x3-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).
Christian Margreitter
1 2 3 4 5 6 7 8 9 10 | # 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 )
|
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
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