[gmx-users] g_hbond on concatenated trajectory

[Carla Jamous]

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> 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.
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