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.
Erik
Carla Jamous skrev 2010-10-15 12.12:
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.
This is the way I'm reading my matrix.
Carla
On Fri, Oct 15, 2010 at 12:09 PM, Erik Marklund <er...@xray.bmc.uu.se
<mailto:er...@xray.bmc.uu.se>> wrote:
Carla Jamous skrev 2010-10-15 12.05:
Hi everyone,
please I need some help on g_hbond.
I concatenated 3 trajectories. I ran g_hbond on the
concatenated trajectory. I got the result of h_bonds.
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
but this same H-bond
doesn't appear in the first 10ps of my concatenated
trajectory's HBmap.
Please does anyone have an idea where I might have done a mistake?
Thank you,
Carla
The first thing to check is if you're reading the matrix upside
down. Sounds trivial, but it's an eaasy mistake to do.
Cheers,
--
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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
er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se>
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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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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