Dear Justin,<br><br>this is my trjcat command<br><br> /home/cocktail/vitalini/gromacs_special/bin/trjcat -f /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_annealing.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_annealing2.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_min.gro /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_min1.gro -o /home/cocktail2/vitalini/reverse_transformation_vacuum/300-65-100/300-65-100_traj_tot.xtc -settime -cat<br>
<br>I'm using the settime command to have each structure at a different time step. If I was using it wrongly please correct me.<br><br>Thanks in advance for all the help.<br><br>Francesca<br><br><div class="gmail_quote">
2012/6/16 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 6/16/12 6:48 AM, francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs Users,<br>
<br>
While making a trajectory connecting different gro files I got the following<br>
output which I don't understand.<br>
<br>
Continue writing frames from<br>
/home/cocktail2/vitalini/<u></u>reverse_transformation_vacuum/<u></u>300-166-160/300-166-160_<u></u>annealing.gro<br>
t=1 ps, frame=0<br>
Last frame 0 time 0.000<br>
WARNING: Frames around t=1.000000 ps have a different spacing than the rest,<br>
might be a gap or overlap that couldn't be corrected automatically.<br>
Reading frames from gro file 'Protein', 15230 atoms.<br>
Reading frame 0 time 0.000<br>
WARNING: Couldn't find a time in the frame.<br>
<br>
Can anyone explain to me the implication of this warning message?<br>
<br>
</blockquote>
<br></div></div>
Trajectories need time information, .gro files don't have any. In the absence of your trjcat command, I can only assume you're not using -settime to specify what time point to which each frame corresponds. If that's not the case, please provide the command you are using.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
==============================<u></u>==========<br>
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Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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<br>
<br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br>Francesca Vitalini<br><br>PhD student at Computational Molecular Biology Group, <br>Department of Mathematics and Informatics, FU-Berlin<br>Arnimallee 6 14195 Berlin<br>
<br><a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br><a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.de</a><br><br>+49 3083875776<br>
+49 3083875412<br><br>