[gmx-users] Help for GNUPlot

[Per Larsson]

Hello!

Please note that xmgrace and gunplot are two different programs and as  
such work in different ways, for example in terms of what types of  
input and output they expect. The xvg-files that Gromacs produces are  
indended for xmgrace, and will not work out-of-the-box with gnuplot.

There are tons of tutorials on the internet on how to use gnuplot, and  
I suggest that you start by following a few of those, learning how to  
first make some simple toy-plots

Cheers
/Per




6 maj 2008 kl. 15.07 skrev s lal badshah:

> 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
> Send instant messages to your online friends http://uk.messenger.yahoo.com 
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