<br><br><div class="gmail_quote">2011/1/7 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Qin Qiao wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
2011/1/7 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div class="im"><br>
<br>
<br>
<br>
Qin Qiao wrote:<br>
<br>
Dear all,<br>
<br>
I came across a problem when I want to make the REMD<br>
trajectories continuous.<br>
<br>
What I did:<br>
<br></div>
1. '<a href="http://demux.pl" target="_blank">demux.pl</a> <<a href="http://demux.pl" target="_blank">http://demux.pl</a>> <<a href="http://demux.pl" target="_blank">http://demux.pl</a>> REMD_0.log' --to get the 'replica_index.xvg'<div class="im">
<br>
<br>
2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux<br>
../replica_index.xvg'<br>
<br>
It seems smooth. But when I check the rmsd of the output<br>
0_resort.xtc, I found it's still discontinuous.. with big jumps<br>
about 0.5nm..! Could you help me to figure out what's wrong?<br>
Thanks a lot.<br>
<br>
<br>
Have you properly accounted for periodicity effects?<br>
<br>
-Justin<br>
<br>
<br>
It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...<br>
<br>
</div></blockquote>
<br>
One iteration of trjconv is not necessarily enough to produce a properly imaged trajectory. What is going on in the trajectory when these spikes are occurring?<br>
<br>
-Justin<br>
<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"></div></blockquote></blockquote><div>In VMD, it just seems to change to a different conformation...<br>
<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">
Best,<br>
<br>
Qin<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<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">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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