[gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

  The tricky part is that if you look at the first line in the file 
hbm.xpm you are looking at the bottom row of the matrix when displayed 
with gimp or after converting to xpm2ps. The same line corresponds to 
the first hbond in hbn.ndx. That sentence in the manual is therefore a 
bit ambiguous.

Erik

Carla Jamous skrev 2010-10-15 13.29:
> I'm sorry I don't understand, because your last answer doesn't 
> correspond to what's written in the manual. I'm using gromacs 4.0.3 
> and the manual says:
>
> -hbm: existence matrix. Ordering is identical to that in -hbn index file.
>
> And yes, my trajectory is concatenated the way I intended to, but I 
> will check anyway.
>
> Carla
>
> On Fri, Oct 15, 2010 at 1:23 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
>
>     Have you confirmed that the concaternation was done the way you
>     intended?
>
>
>     -- 
>     -----------------------------------------------
>     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/
>
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>


-- 
-----------------------------------------------
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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101015/20340368/attachment.html>