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Yes, and it's the y-direction that is tricky. If I'm not mistaken,
the first row in the matrix is the *bottom* line in the graphical
output. Thus, the bottom line in the picture would be the first
hbond in the corresponding index file.<br>
<br>
Erik<br>
<br>
Carla Jamous skrev 2010-10-15 12.12:
<blockquote
cite="mid:AANLkTikLh9Zu6jmSRy45ARuSzfr4+1CUPqo5bVT3V7S-@mail.gmail.com"
type="cite">No, I don't think so because I did an .eps file (with
xpm2ps) that indicates the Time(ps) in x-axis and Hydrogen Bond
Index in y-axis.<br>
This is the way I'm reading my matrix.<br>
<br>
Carla<br>
<br>
<div class="gmail_quote">
On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Carla Jamous skrev 2010-10-15 12.05:
<div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hi everyone,<br>
<br>
please I need some help on g_hbond.<br>
<br>
I concatenated 3 trajectories. I ran g_hbond on the
concatenated trajectory. I got the result of h_bonds.<br>
Then I wanted to run g_hbond on each of my 3
trajectories. Here, I get a different result, it means:
if I take the first 10ps of my concatenated trajectory
and I run g_hbond on these 10ps. I get some H-bonds eg.
Gly(N)...H(gly)...O<br>
but this same
H-bond doesn't appear in the first 10ps of my
concatenated trajectory's HBmap.<br>
<br>
Please does anyone have an idea where I might have done
a mistake?<br>
<br>
Thank you,<br>
Carla<br>
<br>
</blockquote>
</div>
</div>
The first thing to check is if you're reading the matrix
upside down. Sounds trivial, but it's an eaasy mistake to do.<br>
<br>
Cheers,<br>
<br>
-- <br>
-----------------------------------------------<br>
Erik Marklund, PhD student<br>
Dept. of Cell and Molecular Biology, Uppsala University.<br>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
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<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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