The R Journal: accepted article

This article will be copy edited and may be changed before publication.

MDplot: Visualise Molecular Dynamics
Christian Margreitter and Chris Oostenbrink

Abstract The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when large amounts of plots are generated. The graphs that are supported range from those which are standard such as RMSD/RMSF (root-mean-square deviation and root-mean-square fluctuation, respectively) to thermodynamic integration analysis and hydrogen bond monitoring over time and address many commonly used analyses. In this article, we set out the package’s functions, give examples of the function calls and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS and AMBER file formats. Moreover, we also provide a bash interface that allows simple embedding of MDplot into bash scripts as the final analysis step. Availability: The package can be obtained in the latest major version from CRAN (https://cran.r or in the most recent version from the project’s GitHub page at, where feedback is also most welcome. MDplot is published under the GPL-3 license.

Received: 2016-04-30; online 2017-05-10
CRAN packages: MDplot, bio3d, Rknots

CC BY 4.0
This article is licensed under a Creative Commons Attribution 4.0 International license.

  author = {Christian Margreitter and Chris Oostenbrink},
  title = {{MDplot: Visualise Molecular Dynamics}},
  year = {2017},
  journal = {{The R Journal}},
  url = {}