[gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

  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 <erikm at xray.bmc.uu.se 
> <mailto:erikm at 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,
>
>     -- 
>     -----------------------------------------------
>     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
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>     http://folding.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
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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