<meta charset="utf-8"><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Hi Justin,</span><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">I am using Gromacs 4.5 beta-2.</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">gmxcheck with file 1 and file 2 tells me exactly the number of frames I specified.</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">gmxcheck -f File1.xtc</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Frames: 2175</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">gmxcheck -f File2.xtc</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Frames: 1232</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">While after concatenating, it skips the frames and the combined trajectory results in 1266 frames.</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Do you attribute this to Gromacs4.5beta2 version? Is there a possible bug in that version for trjcat?</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Regards,</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Lipi </span></font></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br>
Lipi Thukral wrote:<br>> Dear gmx-users,<br>><br>> I intended to concantanate two trajectories with no similar time frames<br>> i.e., both files have distinct time frames. But once I combine the files<br>> many time frames are skipped, details are as follows:<br>
><br>> File 1 has 2175 frames<br>> File 2 has 1232 frames<br>><br><br>What does gmxcheck tell you about each of these files?<br><br>> I used the following command to concatenate:<br>><br>> trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc<br>
><br>> Now I obtained in total 1266 frames instead of 3407 frames as expected.<br>> When I compared the CombinedFile3 with both File 1 and File 2, I found<br>> that it has somehow taken the first 34 frames from File 1 and rest of<br>
> the frames belongs to File 2 i.e., the last file.<br>><br>> I am unable to understand why trjcat skips the frames inspite of no<br>> similarity. I am using 4.5-beta version of Gromacs. I am also open to<br>> sharing the files, should that be needed.<br>
><br><br>There have been numerous beta versions over the last few years, none of which<br>should necessarily be considered stable. Which beta are you using exactly?<br><br>-Justin<br><br>> Any possible explanation as to why I am obtaining the combined<br>
> trajectory with skipping frames, would be really helpful.<br>><br>> Many Thanks,<br>> Lipi<br>><br><br>--<br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank" style="color: rgb(0, 101, 204); ">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank" style="color: rgb(0, 101, 204); ">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>========================================</span><br><br><div class="gmail_quote">On 26 April 2011 22:41, Lipi Thukral <span dir="ltr"><<a href="mailto:lipi.thukral@gmail.com">lipi.thukral@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear gmx-users,<div><br></div><div>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:</div>
<div><br></div><div>File 1 has 2175 frames</div><div>File 2 has 1232 frames</div><div><br></div><div>I used the following command to concatenate:</div><div><br></div><div>trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc</div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div>
<div>
Any possible explanation as to why I am obtaining the combined trajectory with skipping frames, would be really helpful.</div><div><br></div><div>Many Thanks,</div><div>Lipi</div>
</blockquote></div><br></div>