rmsd {MDplot}

Root-mean-square-deviation (RMSD) plot

Description

Plot (multiple) RMSD file(s) as produced by molecular dynamics packages.

Usage

rmsd( rmsdData,
      printLegend = TRUE,
      snapshotsPerTimeInt = 1000,
      timeUnit = "ns",
      rmsdUnit = "nm",
      colours = NA,
      names = NA,
      legendPosition = "bottomright",
      barePlot = FALSE,
      ... )

Arguments

rmsdData

List of (alternating) indices and RMSD values, as produced e.g. by load_rmsd().

printLegend

Boolean, which triggers plotting of the legend.

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.

colours

Vector of colours used for plotting.

names

Vector of the names of the trajectories.

legendPosition

Indicates position of legend: either "bottomright", "bottomleft", "topleft" or "topright".

barePlot

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

...

Additional arguments (ellipsis).

Value

Returns a list of lists, where each sub-list represents a RMSD curve and contains:

minValue

The minimum value over the whole time range.

maxValue

The maximum value over the whole time range.

meanValue

The mean value calculated over the whole time range.

sd

The standard deviation calculated over the whole time range.

Author(s)

Christian Margreitter

Examples

# GROMOS (see load_rmsd() for other input possibilities)
rmsd( load_rmsd( c( system.file( "extdata/rmsd_example_1.txt.gz", package = "MDplot" ),
                    system.file( "extdata/rmsd_example_2.txt.gz", package = "MDplot" ) ) ) )