Plotting Xmgrace (.xvg) Files#

The GROMACS molecular dynamics software bundles numerous analysis tools. The output from these are in (.xvg) format to be viewed with xmgrace. Although xmgrace has some powerful tools for quick calculation of mean standard deviation, etc., the plots are cumbersome to deal with and difficult to compare multiple files.

MD DaVis provides the command xvg to plot such files using plotly or matplotlib.

The .xvg files are space or tab delimited text files with time and data in the first and second columns, respectively.

# gmx rms is part of G R O M A C S:
#
# Gromacs Runs On Most of All Computer Systems
#
@    title "RMSD"
@    xaxis  label "Time (ps)"
@    yaxis  label "RMSD (nm)"
@TYPE xy
@ subtitle "System after lsq fit to System"
   0.0000000    0.0000031
  10.0000000    0.0677038
  20.0000000    0.0837483
  30.0000000    0.0894995

MD DaVis can also plot multiple Grace (.xvg) files, which is the format for the output files from many GROMACS analysis tools. For example, an interactive plot with RMSD and RG from multiple trajectories can be created for quick comparison.

md-davis xvg <path/to/file.xvg>

Replace <path/to/file.xvg> with the location of your .xvg file.

Create interactive plot for time series data: root mean squared deviation (RMSD) and radius of gyration (R:subscript: G)

Note

The titles and axis labels are parsed from the lines in the xvg file starting with @. It is expected that the when plotting multiple xvg files, they contain the same kind of data. Therefore, the titles and axis labels in the last supplied file are used.

md-davis xvg#

Plot xmgrace (.xvg) files generated by GROMACS.

Arguments:

xvg_files (Files): Input xmgrace (.xvg) files’

md-davis xvg [OPTIONS] XVG_FILES...

Options

-o, --output <output>#: Output filename

--matplotlib, --plotly#: Use plotly for plotting

Arguments

XVG_FILES#: Required argument(s)

Table of Contents

Plotting Xmgrace (.xvg) Files#

md-davis xvg#