<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Dear David,</span></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
<span style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">Dear Justin,</span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><span style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">I have now installed the latest version of Gromacs 4.5.4. The problem still persists. </span></div>
<div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">The two files to concatenate do not have exactly the same timeframes. However they do have something like the following:</div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px">
<br></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">File 1: 2091000.0000000</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">File 2: 2090170.0000000</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;">May be I don't understand but its clear that the two files do not have the same time-frames so why is trjcat skipping the frames?</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><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div style="border-collapse:collapse;font-family:arial, sans-serif;font-size:13px"><br></div><font face="arial, sans-serif"><span style="border-collapse:collapse">On 4/27/2011 3:51 PM, Lipi Thukral wrote:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Hi Justin,</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> I am using Gromacs 4.5 beta-2.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> gmxcheck with file 1 and file 2 tells me exactly the number of frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> I specified.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> gmxcheck -f File1.xtc</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Frames: 2175</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> gmxcheck -f File2.xtc</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Frames: 1232</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> While after concatenating, it skips the frames and the combined</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> trajectory results in 1266 frames.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Do you attribute this to Gromacs4.5beta2 version? Is there a possible</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> bug in that version for trjcat?</span></font><br><br><font face="arial, sans-serif"><span style="border-collapse:collapse">Maybe - but it's not worth finding out whether a bug existed then.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">There's no value in trouble-shooting a beta version that is known to</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">have other problems. Get the latest GROMACS version and install and use</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">it. If you can demonstrate a problem there, now people will be much more</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">interested in addressing the issue.</span></font><br>
<br><font face="arial, sans-serif"><span style="border-collapse:collapse">Mark</span></font><br><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Regards,</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Lipi</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Lipi Thukral wrote:</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > Dear gmx-users,</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > I intended to concantanate two trajectories with no similar time frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > i.e., both files have distinct time frames. But once I combine the files</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > many time frames are skipped, details are as follows:</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > File 1 has 2175 frames</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> > File 2 has 1232 frames</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> What does gmxcheck tell you about each of these files?</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > I used the following command to concatenate:</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > trjcat -f File1.xtc File2.xtc -o CombinedFile3.xtc</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > Now I obtained in total 1266 frames instead of 3407 frames as expected.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > When I compared the CombinedFile3 with both File 1 and File 2, I found</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> > that it has somehow taken the first 34 frames from File 1 and rest of</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > the frames belongs to File 2 i.e., the last file.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > I am unable to understand why trjcat skips the frames inspite of no</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> > similarity. I am using 4.5-beta version of Gromacs. I am also open to</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > sharing the files, should that be needed.</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> There have been numerous beta versions over the last few years, none</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> of which</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> should necessarily be considered stable. Which beta are you using</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> exactly?</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> -Justin</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > Any possible explanation as to why I am obtaining the combined</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> > trajectory with skipping frames, would be really helpful.</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> > Many Thanks,</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> > Lipi</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ></span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> --</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> ==============================</span></font><font face="arial, sans-serif"><span style="border-collapse:collapse">==========</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Justin A. Lemkul</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Ph.D. Candidate</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ICTAS Doctoral Scholar</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> MILES-IGERT Trainee</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Department of Biochemistry</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> Virginia Tech</span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> Blacksburg, VA</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> jalemkul[at]</span></font><a href="http://vt.edu/" style="color:rgb(0, 101, 204);border-collapse:collapse;font-family:arial, sans-serif;font-size:13px" target="_blank">vt.edu</a><font face="arial, sans-serif"><span style="border-collapse:collapse"> <</span></font><a href="http://vt.edu/" style="color:rgb(0, 101, 204);border-collapse:collapse;font-family:arial, sans-serif;font-size:13px" target="_blank">http://vt.edu/</a><font face="arial, sans-serif"><span style="border-collapse:collapse">> | (540) 231-9080</span></font><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">> </span></font><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" style="color:rgb(0, 101, 204);border-collapse:collapse;font-family:arial, sans-serif;font-size:13px" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<font face="arial, sans-serif"><span style="border-collapse:collapse">></span></font><br><font face="arial, sans-serif"><span style="border-collapse:collapse">> ==============================</span></font><font face="arial, sans-serif"><span style="border-collapse:collapse">==========</span></font>