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

[Lipi Thukral]

Hi Justin,

I am using Gromacs 4.5 beta-2.
gmxcheck with file 1 and file 2 tells me exactly the number of frames I
specified.
gmxcheck -f File1.xtc
Frames: 2175

gmxcheck -f File2.xtc
Frames: 1232

While after concatenating, it skips the frames and the combined trajectory
results in 1266 frames.
Do you attribute this to Gromacs4.5beta2 version? Is there a possible bug in
that version for trjcat?

Regards,
Lipi

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
>

--
========================================

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

========================================

On 26 April 2011 22:41, Lipi Thukral <lipi.thukral at gmail.com> 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
>
> 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.
>
>  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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