Yes I do have a trajectory and gmxcheck doesn't complain,<br>this is the output<br><br>Checking file ./300-65-100/300-65-100_traj_tot.xtc<br>Reading frame 0 time 1.000 <br># Atoms 15230<br>Precision 0.001 (nm)<br>
Last frame 3 time 4.000 <br><br><br>Item #frames Timestep (ps)<br>Step 4 1<br>Time 4 1<br>Lambda 0<br>Coords 4 1<br>Velocities 0<br>Forces 0<br>
Box 4 1<br><br>gcq#20: "Check Your Output" (P. Ahlstrom)<br><br><br>I was just wandering if the warning had any implication for the later use of the trajectory.<br><br>Thank you very much for your help<br>
<br>Francesca<br><br><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="im"><br>
<br>
On 6/16/12 7:54 AM, francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
yes and I do.<br>
By the way the version of GROMACS I'm using is the 3.3.1, I forgot to specify<br>
that before.<br>
<br>
</blockquote>
<br></div>
OK, I see the same with version 4.5.5, but a trajectory is produced from my set of .gro files and it is correct.<br>
<br>
Continue writing frames from md_0_25.gro t=0 ps, frame=0<div class="im"><br>
Last frame 0 time 0.000<br></div>
WARNING: Frames around t=0.000000 ps have a different spacing than the rest,<div class="im"><br>
might be a gap or overlap that couldn't be corrected automatically.<br></div>
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.<div class="im"><br>
Reading frame 0 time 0.000<br>
WARNING: Couldn't find a time in the frame.<br>
<br></div>
lasttime 0<br>
<br>
Continue writing frames from md_25_50.gro t=25 ps, frame=1<div class="im"><br>
Last frame 0 time 0.000<br></div>
WARNING: Frames around t=25.000000 ps have a different spacing than the rest,<div class="im"><br>
might be a gap or overlap that couldn't be corrected automatically.<br></div>
Reading frames from gro file 'Raft G96 system in water', 60523 atoms.<div class="im"><br>
Reading frame 0 time 0.000<br>
WARNING: Couldn't find a time in the frame.<br>
<br></div>
lasttime 25<br>
<br>
The key is to note that it is setting the times specified. Do you get an .xtc file? What does gmxcheck tell you about it?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2012/6/16 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>
On 6/16/12 7:41 AM, francesca vitalini wrote:<br>
<br>
Dear Justin,<br>
<br>
this is my trjcat command<br>
<br></div>
/home/cocktail/vitalini/__<u></u>gromacs_special/bin/trjcat -f<br>
/home/cocktail2/vitalini/__<u></u>reverse_transformation_vacuum/<u></u>__300-65-100/300-65-100___<u></u>annealing.gro<br>
/home/cocktail2/vitalini/__<u></u>reverse_transformation_vacuum/<u></u>__300-65-100/300-65-100___<u></u>annealing2.gro<br>
/home/cocktail2/vitalini/__<u></u>reverse_transformation_vacuum/<u></u>__300-65-100/300-65-100_min.<u></u>gro<br>
/home/cocktail2/vitalini/__<u></u>reverse_transformation_vacuum/<u></u>__300-65-100/300-65-100_min1.<u></u>gro<br>
-o<br>
/home/cocktail2/vitalini/__<u></u>reverse_transformation_vacuum/<u></u>__300-65-100/300-65-100_traj__<u></u>_tot.xtc<div class="im"><br>
-settime -cat<br>
<br>
I'm using the settime command to have each structure at a different time<br>
step.<br>
If I was using it wrongly please correct me.<br>
<br>
<br>
You should be prompted to then set a time value for each frame, is that not<br>
the case?<br>
<br>
<br>
-Justin<br>
<br>
--<br></div>
==============================<u></u>__==========<div class="im"><br>
<br>
Justin A. Lemkul, Ph.D.<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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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>
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</blockquote><div class="HOEnZb"><div class="h5">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
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>
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</div></div></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>