Thank you Justin for your advice,<br><br>I did gmxcheck on the non-concatenated trajectory and found that my trajectory is not corrupted.<br>I did re-run trjcat, without any problem. But when I run trjconv, it gives the same error message as before.<br>
It's really strange because I'm sure that my trajectory is ok (with gmxcheck)!<br><br>Please do you have another idea?<br><br>Thanks,<br>Carla<br><br><div class="gmail_quote">On Thu, Sep 2, 2010 at 3:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;"><div><div></div><div class="h5"><br>
<br>
Carla Jamous wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi everyone,<br>
<br>
I concatenated many trajectories with trjcat and didn't have any problem.<br>
But when I did trjconv, I had this warning:<br>
<br>
WARNING: Incomplete frame: nr 6077 time 12154<br>
<br>
so I tried to do gmxcheck on my concatenated .xtc and got :<br>
<br>
Reading frame 0 time 0.000 # Atoms 192409<br>
Precision 0.001 (nm)<br>
Reading frame 6000 time 12000.001 WARNING: Incomplete frame: nr 6077 time 12154<br>
<br>
<br>
Item #frames Timestep (ps)<br>
Step 6077 2<br>
Time 6077 2<br>
Lambda 0<br>
Coords 6077 2<br>
Velocities 0<br>
Forces 0<br>
Box 6077 2<br>
<br>
please can anyone tell me what might be the problem, knowing that when I gmxcheck the file .xtc that contains this frame, I don't get a warning.<br>
<br>
</blockquote>
<br></div></div>
Two possibilities:<br>
<br>
1. trjcat corrupted the frame when trying to write the full trajectory<br>
2. The original non-concatenated trajectory is corrupted and trjcat passed over the problem, while trjconv cannot.<br>
<br>
Check the original (non-concatenated) trajectories to assess their integrity. If #1 is true, run trjcat again. If #2 is true, you cannot use the corrupted frame(s), which may mean re-running from a point prior to the corruption.<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;">
Thank you,<br>
Carla<br>
<br>
</blockquote>
<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>
<br>
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