[gmx-users] Help for GNUPlot

[Zoltan Varga]

Hi,

Actually gnuplot can plot the xvg files without any modification. It skips all the lines in the file which is not compatible with the command: u 1:2
The problem is the missing word about how to draw the data. Maybe you have also recognized it meanwhile. In the correct form:
>plot "rmsf.xvg" u 1:2 w lines

Zoltan 

s lal badshah <shahbiochemist at yahoo.com> wrote: Dear Mark,
Hi ! Currently I tried to install xmgrace but the toolbar menue is not shown on window screen so I am using gnuplot for analysis as I have little know how about unix/linux.Please set to me the following.
hmad at uop:~> cd project
ahmad at uop:~/project> ls
#bfac.pdb.1#   conf.pdb      genion.log  md323.tpr     pr.edr     topol_A.itp
#rmsf.xvg.1#   dist.xvg      gyrate.xvg  md323.trr     pr.gro     topol_B.itp
#topol.top.1#  distance.xvg  index.ndx   md323.xtc     pr.log     traj.trr
#traj.trr.1#   em.mdp        ions.pdb    md323lie.xvg  pr.mdp     water.pdb
2a5f.pdb        em.pdb        md323.edr   mdout.mdp     pr.tpr
bfac.pdb       em.tpr        md323.gro   pe.xvg        pr.trr
bonds.xvg      ener.edr      md323.log   posre_A.itp   rmsf.xvg
box.pdb        energy.xvg    md323.mdp   posre_B.itp   topol.top
ahmad at uop:~/project> gnuplot

        G N U P L O T
        Version 4.2 patchlevel 0
        last modified March 2007
        System: Linux 2.6.22.5-31-default

        Copyright (C) 1986 - 1993, 1998, 2004,  2007
        Thomas Williams, Colin Kelley and many others

        Type `help` to access the on-line reference manual.
        The gnuplot FAQ is available from
                http://www.gnuplot.info/faq/

        Send comments and help requests to  <gnuplot-info at lists.sourceforge.net>
        Send bug reports and suggestions to <gnuplot-bugs at lists.sourceforge.net>


Terminal type set to 'x11'
gnuplot> plot "rmsf.xvg" u 1:2 w 
         ^
         expecting 'lines', 'points', 'linespoints', 'dots', 'impulses',
        'yerrorbars', 'xerrorbars',  'xyerrorbars', 'steps', 'fsteps',
        'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars',
        'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines',
        'yerrorlines', 'xyerrorlines', 'pm3d', 'labels', 'histograms',
         'image', 'rgbimage'

gnuplot> boxes
         ^
         invalid command

gnuplot> plot lines "rmsf.xvg" u 1:2 w 
         undefined variable: lines

gnuplot> plot gyrate.xvg
         undefined variable: gyrate

gnuplot> plot "gyrate.xvg"
               ^
         Bad data on line 9

gnuplot> 
Regards,
Lal badshah
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