md_davis xvg¶
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.
It is generally intended that the when plotting multiple xvg files, they contain the same kind of data. Therefore, the titles and axes labels in the last supplied file are used.
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)
<iframe src=”/_static/acylphosphatase_rmsg_rg.html” frameborder=”0” width=”100%” height=”500px”></iframe>