Gromacs

Plotting Data

    Table of contents
    1. 1. Software
    2. 2. Future Developments

    The various GROMACS analysis utilities can generate .xvg files. These are text files that have been specifically formated for direct use in Grace. You can, however, in all GROMACS analysis programs turn off the Grace specific codes by running the programs with the -xvg none option. This circumvents problems with tools like gnuplot and Excel (see below).

    Note that Grace uses some embedded backslash codes to indicate superscripts, normal script, etc. in units. So "Area (nm\S2\N)" is nm squared. 

     

    Software

    Some software packages that can be used to graph data in a .xvg file:

    • Grace - WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix-like OS, provided that you can satisify its library dependencies (Lesstif is a valid free alternative to Motif). As well, it has been successfully ported to VMS, OS/2, and Win9*/NT/2000/XP (some minor functionality may be missing, though)
    • gnuplot - portable command-line driven interactive data and function plotting utility for UNIX, IBM OS/2, MS Windows, DOS, Macintosh, VMS, Atari and many other platforms. Remember to use
      set datafile commentschars "#@&"
      
      to avoid gnuplot trying to interpret Grace-specific commands in the .xvg file or use the -xvg none option when running the analysis program. For simple usage,
      plot "file.xvg" using 1:2 with lines
      
      is a hack that will achieve the right result.
    • MS Excel - change the file extension to .csv and open the file (when prompted, choose to ignore the first 20 or so rows and select fixed-width columns, if you are using German MS Excel version, you have to change decimal delimiter from "," to ".", or use your favorite *nix tool.
    • Sigma Plot A commercial tool for windows with some useful analysis tools in it.
    • R - freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.
    • SPSS A commercial tool (Statistical Product and Service Solutions), which can also plot and analyse data.

    Future Developments

    • It would be nice to be able to interconvert between different output formats (xpm to ascii).
    • It would also be great to be able to chain different analysis tools from a scripting language (e.g. Python) but this requires significant amount of work. The idea would be to make most/all analysis tools able to process just one coordinate set.
    • Dynamic index files - files that do not contain atom numbers but just a query
    Page last modified 12:59, 21 Mar 2012 by mabraham