[gmx-users] Probable error in trjcat; skipping frames

[Justin A. Lemkul]

Lipi Thukral wrote:
> Dear gmx-users,
> 
> I intended to concantanate two trajectories with no similar time frames 
> i.e., both files have distinct time frames. But once I combine the files 
> many time frames are skipped, details are as follows:
> 
> File 1 has 2175 frames
> File 2 has 1232 frames
> 

What does gmxcheck tell you about each of these files?

> I used the following command to concatenate:
> 
> trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc
> 
> Now I obtained in total 1266 frames instead of 3407 frames as expected. 
> When I compared the CombinedFile3 with both File 1 and File 2, I found 
> that it has somehow taken the first  34 frames from File 1 and rest of 
> the frames belongs to File 2 i.e., the last file.
> 
> I am unable to understand why trjcat skips the frames inspite of no 
> similarity. I am using 4.5-beta version of Gromacs. I am also open to 
> sharing the files, should that be needed.
> 

There have been numerous beta versions over the last few years, none of which 
should necessarily be considered stable.  Which beta are you using exactly?

-Justin

> Any possible explanation as to why I am obtaining the combined 
> trajectory with skipping frames, would be really helpful.
> 
> Many Thanks,
> Lipi
> 

-- 
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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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