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

[Mark Abraham]

On 4/27/2011 3:51 PM, Lipi Thukral wrote:
> 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?

Maybe - but it's not worth finding out whether a bug existed then. 
There's no value in trouble-shooting a beta version that is known to 
have other problems. Get the latest GROMACS version and install and use 
it. If you can demonstrate a problem there, now people will be much more 
interested in addressing the issue.

Mark

>
> 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 <http://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 
> <mailto: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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