Abstract
The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.
Highlights
The amount of data produced by molecular dynamics (MD) engines (such as GROMOS (Schmid et al, 2012; Eichenberger et al, 2011), GROMACS (Pronk et al, 2013), NAMD (Phillips et al, 2005), AMBER (Cornell et al, 1995), and CHARMM (Brooks et al, 2009)) has been constantly increasing over recent years
There have been attempts made in that direction, for example the package bio3d (Grant et al, 2006; Skjærven et al, 2014) (which allows the trajectories to be processed in terms of principle component analysis (PCA), root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) calculations), MDtraj (McGibbon et al, 2015), or Rknots (Comoglio and Rinaldi, 2012)
Return value: Returns an n × 2-matrix, with the first column being the list of hydrogen bond identifiers plotted and the second one the occurrence over the selected time range
Summary
The amount of data produced by molecular dynamics (MD) engines (such as GROMOS (Schmid et al, 2012; Eichenberger et al, 2011), GROMACS (Pronk et al, 2013), NAMD (Phillips et al, 2005), AMBER (Cornell et al, 1995), and CHARMM (Brooks et al, 2009)) has been constantly increasing over recent years. An example would be the plotting of a time series of a clustering program or hydrogen bonds. The plotting functions return useful information on the data used, e.g., range, mean and standard deviation of curves. Return value: Returns a summary (n + 1) × m-matrix with n being the number of input trajectories and m the number of different clusters (which have been plotted).
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