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

[David van der Spoel]

On 2011-04-27 07.51, 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?
it combines the trajectories. If you have frames with the same timestamp 
in both trajs it will use only one of those.
>
> 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
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se