[gmx-users] incomplete frame

[Carla Jamous]

Thank you Justin for your advice,

I did gmxcheck on the non-concatenated trajectory and found that my
trajectory is not corrupted.
I did re-run trjcat, without any problem. But when I run trjconv, it gives
the same error message as before.
It's really strange because I'm sure that my trajectory is ok (with
gmxcheck)!

Please do you have another idea?

Thanks,
Carla

On Thu, Sep 2, 2010 at 3:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Carla Jamous wrote:
>
>> Hi everyone,
>>
>> I concatenated many trajectories with trjcat and didn't have any problem.
>> But when I did trjconv, I had this warning:
>>
>> WARNING: Incomplete frame: nr 6077 time 12154
>>
>> so I tried to do gmxcheck on my concatenated .xtc and got :
>>
>> Reading frame       0 time    0.000  # Atoms  192409
>> Precision 0.001 (nm)
>> Reading frame    6000 time 12000.001  WARNING: Incomplete frame: nr 6077
>> time 12154
>>
>>
>> Item        #frames Timestep (ps)
>> Step          6077    2
>> Time          6077    2
>> Lambda           0
>> Coords        6077    2
>> Velocities       0
>> Forces           0
>> Box           6077    2
>>
>> please can anyone tell me what might be the problem, knowing that when I
>> gmxcheck the file .xtc that contains this frame, I don't get a warning.
>>
>>
> Two possibilities:
>
> 1. trjcat corrupted the frame when trying to write the full trajectory
> 2. The original non-concatenated trajectory is corrupted and trjcat passed
> over the problem, while trjconv cannot.
>
> Check the original (non-concatenated) trajectories to assess their
> integrity. If #1 is true, run trjcat again.  If #2 is true, you cannot use
> the corrupted frame(s), which may mean re-running from a point prior to the
> corruption.
>
> -Justin
>
>  Thank you,
>> Carla
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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