Hi,<br><br>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<br>The problem is the missing word about how to draw the data. Maybe you have also recognized it meanwhile. In the correct form:<br>>plot "rmsf.xvg" u 1:2 w lines<br><br>Zoltan <br><br><b><i>s lal badshah <shahbiochemist@yahoo.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Dear Mark,<br>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.<br>hmad@uop:~> cd project<br>ahmad@uop:~/project> ls<br>#bfac.pdb.1# conf.pdb genion.log md323.tpr pr.edr
topol_A.itp<br>#rmsf.xvg.1# dist.xvg gyrate.xvg md323.trr pr.gro topol_B.itp<br>#topol.top.1# distance.xvg index.ndx md323.xtc pr.log traj.trr<br>#traj.trr.1# em.mdp ions.pdb md323lie.xvg pr.mdp water.pdb<br>2a5f.pdb em.pdb md323.edr mdout.mdp pr.tpr<br>bfac.pdb em.tpr md323.gro pe.xvg pr.trr<br>bonds.xvg ener.edr md323.log posre_A.itp
rmsf.xvg<br>box.pdb energy.xvg md323.mdp posre_B.itp topol.top<br>ahmad@uop:~/project> gnuplot<br><br> G N U P L O T<br> Version 4.2 patchlevel 0<br> last modified March 2007<br> System: Linux 2.6.22.5-31-default<br><br> Copyright (C) 1986 - 1993, 1998, 2004, 2007<br> Thomas Williams, Colin Kelley and many others<br><br> Type `help` to access the on-line reference manual.<br> The gnuplot FAQ is available from<br>
http://www.gnuplot.info/faq/<br><br> Send comments and help requests to <gnuplot-info@lists.sourceforge.net><br> Send bug reports and suggestions to <gnuplot-bugs@lists.sourceforge.net><br><br><br>Terminal type set to 'x11'<br>gnuplot> plot "rmsf.xvg" u 1:2 w <br> ^<br> expecting 'lines', 'points', 'linespoints', 'dots', 'impulses',<br> 'yerrorbars', 'xerrorbars', 'xyerrorbars', 'steps', 'fsteps',<br> 'histeps', 'filledcurves', 'boxes', 'boxerrorbars', 'boxxyerrorbars',<br> 'vectors', 'financebars', 'candlesticks', 'errorlines', 'xerrorlines',<br> 'yerrorlines', 'xyerrorlines', 'pm3d', 'labels',
'histograms',<br> 'image', 'rgbimage'<br><br>gnuplot> boxes<br> ^<br> invalid command<br><br>gnuplot> plot lines "rmsf.xvg" u 1:2 w <br> undefined variable: lines<br><br>gnuplot> plot gyrate.xvg<br> undefined variable: gyrate<br><br>gnuplot> plot "gyrate.xvg"<br> ^<br> Bad data on line 9<br><br>gnuplot> <br>Regards,<br>Lal badshah<br><div> Send instant messages to your online friends http://uk.messenger.yahoo.com _______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at
http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</div></blockquote><br><p> 
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