[gmx-users] incomplete frame

[Mark Abraham]

----- 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
 > 
>  ========================================
>  -- 
>  gmx-users mailing list    gmx-users at gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
>  Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 > 
 > -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search 
> before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100903/b4bf862c/attachment.html>