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 <[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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