[gmx-users] incomplete frame

[Justin A. Lemkul]

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
> 

-- 
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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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