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<p class="MsoNormal"><span style="color:#1F497D">Dear Mark, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Many thanks for taking the time to answer my question.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I’ve had a look at the link. However, as the g_helixorient output files are a little “unconventional-looking”, I am not sure if gnuplot could handle them.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">This is how my bending.xvg file looks like when I view it on my linux terminal<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 0 0 0 15.5414686203 13.9671831131 5.49754190445 1.83397710323 4.68<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">052530289 0.683569073677 4.43345403671 8.25963497162 5.08707904816 13.3334512711 7.34296607971 2.19187068<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">939 2.44664645195 0.202708780766 3.66099739075 10.3064308167 4.37143564224 0.971765637398 12.6073293686<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">81.1007080078 66.1958847046 28.0650749207 12.9960222244 16.3757514954 0 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 100.000007629 0 0 2.19846844673 3.11483025551 0.664996445179 1.77089393139 5.45<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">826148987 5.11829614639 2.50709962845 2.90959501266 4.06375169754 9.80808544159 12.7944087982 2.6745197<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">773 4.58594942093 1.63769423962 2.60466551781 0.494560062885 5.87983322144 2.39179229736 17.8020935059<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">89.3860473633 78.2087173462 22.6202278137 7.18984699249 2.18211603165 0 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 200.000015259 0 0 11.4898967743 14.8035535812 11.0557250977 4.95649862289 5.58<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">447694778 8.45914077759 5.94662857056 0.607162833214 2.6271879673 8.9500579834 2.29822874069 7.87417221<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">069 0.892409682274 7.41711711884 2.01197814941 7.29352807999 3.83971619606 0.767958164215 15.4690599442<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">87.5663528442 73.4160614014 24.1331748962 8.33314704895 2.42648363113 0 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> 300 0 0 12.7444248199 11.3533630371 6.02183914185 2.64138007164 1.24<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">458372593 0.375344187021 2.73659491539 4.94989299774 5.81749725342 16.2174777985 8.22213363647 4.51266765<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">594 4.29477596283 7.25417470932 12.5503282547 5.51523017883 4.4407377243 9.50404548645 17.9626598358… … …<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I have played with other options too e.g. axis.dat, center.dat, radius.xvg, rise.xvg, rot.xvg etc. they all look like the above.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Any help is very much appreciated.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks again,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Huiwen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Thursday, November 24, 2011 10:39 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Visualizing g_helixorient output<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On 23/11/2011 8:59 PM, NG HUI WEN wrote: <o:p></o:p></p>
<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I have a follow up question from this recent post <a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html">
http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html</a> regarding the visualization of g_helixorient output.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">According to the post, one needs to use xmgrace with –nxy to view the data properly. I have not got the xmgrace program installed and am just wondering if one could use programs like gnuplot (with some special commands perhaps) instead?<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><br>
Yes, you will be able to generate a plot. See <a href="http://www.gromacs.org/Documentation/How-tos/Graphing_Data">
http://www.gromacs.org/Documentation/How-tos/Graphing_Data</a><br>
<br>
Mark<o:p></o:p></span></p>
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