[gmx-users] incomplete frame
Mark Abraham
mark.abraham at anu.edu.au
Fri Sep 3 10:35:58 CEST 2010
----- 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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