rmsd function

Root-mean-square-deviation (RMSD) plot

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

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).

Returns

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.

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" ) ) ) )

Author(s)

Christian Margreitter