[gmx-users] Help for GNUPlot

[Florian Haberl]

Hi,


On Tuesday, 6. May 2008 15:07, s lal badshah 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
>
>  Send instant messages to your online friends http://uk.messenger.yahoo.com

take a look on your data file

less rmsf.xvg 

first 12 lines or so are without data. It is the header for xmgrace, so you 
have to ignore them your delete out of the file.

You can also analyse the data with the flag -noxvgr, than it will be written 
without xmgrace header.

A good starting point for gnuplot is 

http://www.gnuplot.info/help.html



greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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