MDplot (version 1.0.1)

rmsd_average: Root-mean-square-deviation (RMSD) average plot

Description

Combines several RMSD index-value pairs and computes and plots the mean value and the spread (the respective minimum and maximum values) at every timepoint. This function is particularly useful, when multiple identical simulation runs (replicates) need to be analysed since it shows a 'corridor' which allows interpretation e.g. of the overall stability.

Usage

rmsd_average( rmsdInput,
              levelFactor = NA,
              snapshotsPerTimeInt = 1000,
              timeUnit = "ns",
              rmsdUnit = "nm",
              maxYAxis = NA,
              barePlot = FALSE,
              ... )

Arguments

rmsdInput

List of input tables (which are provided by function load_rmsd()).

levelFactor

If there are many datapoints, this parameter may be used to use only the levelFactorth datapoints to obtain a nicer graph.

snapshotsPerTimeInt

Number, specifying how many snapshots are comprising one timeUnit.

timeUnit

Specifies, which unit the x-axis is given in.

rmsdUnit

Specifies, which unit the y-axis is given in.

maxYAxis

Can be used to manually set the y-axis of the plot.

barePlot

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

...

Additional arguments (ellipsis).

Value

Returns a nx4-matrix, with the rows representing different snapshots and the columns the respective values as follows:

• minimum The minimum RMSD value over all input sources at a given time.

• mean The mean RMSD value over all input sources at a given time.

• maximum The maximum RMSD value over all input sources at a given time.

Examples

# GROMOS (see load_rmsd() for other input possibilities)
rmsd_average( list( load_rmsd( system.file( "extdata/rmsd_example_1.txt.gz",
                                            package = "MDplot" ) ),
                    load_rmsd( system.file( "extdata/rmsd_example_2.txt.gz",
                                            package = "MDplot" ) ) ),
              snapshotsPerTimeInt = 2000, maxYAxis = 0.445 )