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 <[email protected]
<mailto:[email protected]>> 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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