[gmx-users] incomplete frame

[Carla Jamous]

I didn't un out of disk space but the size of my concatenated .xtc file is 4
GB.
Why? the size of my file affects trjconv?

Carla

On Fri, Sep 3, 2010 at 10:35 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> ----- Original Message -----
> From: Carla Jamous <carlajamous at gmail.com>
> Date: Friday, September 3, 2010 18:31
> Subject: Re: [gmx-users] incomplete frame
> To: jalemkul at vt.edu, Discussion list for GROMACS users <
> gmx-users at gromacs.org>
>
> > 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?
>
> Have you run out of disk space, or run into a 2GB file size limit?
>
> Mark
>
>
> >
> > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>> > ========================================
>> > --
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