[gmx-users] g_hbond on concatenated trajectory

[Erik Marklund]

  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    http://folding.bmc.uu.se/