[gmx-users] Visualizing g_helixorient output

Thu Nov 24 03:50:50 CET 2011

Dear Mark,

Many thanks for taking the time to answer my question.

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.

This is how my bending.xvg file looks like when I view it on my linux terminal

              0                0                0    15.5414686203    13.9671831131    5.49754190445    1.83397710323    4.68
052530289   0.683569073677    4.43345403671    8.25963497162    5.08707904816    13.3334512711    7.34296607971    2.19187068
939    2.44664645195   0.202708780766    3.66099739075    10.3064308167    4.37143564224   0.971765637398    12.6073293686
81.1007080078    66.1958847046    28.0650749207    12.9960222244    16.3757514954                0                0
  100.000007629                0                0    2.19846844673    3.11483025551   0.664996445179    1.77089393139    5.45
826148987    5.11829614639    2.50709962845    2.90959501266    4.06375169754    9.80808544159    12.7944087982     2.6745197
773    4.58594942093    1.63769423962    2.60466551781   0.494560062885    5.87983322144    2.39179229736    17.8020935059
89.3860473633    78.2087173462    22.6202278137    7.18984699249    2.18211603165                0                0
  200.000015259                0                0    11.4898967743    14.8035535812    11.0557250977    4.95649862289    5.58
447694778    8.45914077759    5.94662857056   0.607162833214     2.6271879673     8.9500579834    2.29822874069    7.87417221
069   0.892409682274    7.41711711884    2.01197814941    7.29352807999    3.83971619606   0.767958164215    15.4690599442
87.5663528442    73.4160614014    24.1331748962    8.33314704895    2.42648363113                0                0
            300                0                0    12.7444248199    11.3533630371    6.02183914185    2.64138007164    1.24
458372593   0.375344187021    2.73659491539    4.94989299774    5.81749725342    16.2174777985    8.22213363647    4.51266765
594    4.29477596283    7.25417470932    12.5503282547    5.51523017883     4.4407377243    9.50404548645    17.9626598358... ... ...

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.

Any help is very much appreciated.

Thanks again,
Huiwen

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, November 24, 2011 10:39 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Visualizing g_helixorient output

On 23/11/2011 8:59 PM, NG HUI WEN wrote:
Dear all,

I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output.

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?

Yes, you will be able to generate a plot. See http://www.gromacs.org/Documentation/How-tos/Graphing_Data

Mark
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