[gmx-users] incomplete frame

[Mark Abraham]

----- Original Message -----
From: Carla Jamous <carlajamous at gmail.com>
Date: Friday, September 3, 2010 18:40
Subject: Re: [gmx-users] incomplete frame
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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?

No, if the filesystem (e.g. the Windows-95-era FAT32 filesystem, see http://en.wikipedia.org/wiki/File_Allocation_Table) simply cannot cope with a file that large, and doesn't return an error when the limit is met, then trjcat will think it has succeeded in writing a larger file. Then, later, trjconv observes the erroneous condition. Presumably, the solution is using a real filesystem. :-)

Mark

> 
> 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
  > > 
> >  ========================================
 > >  -- 
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