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On 4/27/2011 3:51 PM, Lipi Thukral wrote:
<blockquote
cite="mid:BANLkTimm9tT0UyCEPWHG8mT8=xAmGAk2_w@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimm9tT0UyCEPWHG8mT8=xAmGAk2_w@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true" href="http://vt.edu/"
target="_blank" style="color: rgb(0, 101, 204);">vt.edu</a> |
(540) 231-9080<br>
<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:lipi.thukral@gmail.com">lipi.thukral@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
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>
</blockquote>
<br>
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