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

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 26 22:46:38 CEST 2011

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?


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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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