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