Hello Justin,<br><br>I am using Gromacs 4.0.7<br>Actually, I am joining around 20 trajectories of around 300 ns each. Its a CGMD run. But I reported here only those two trajectories between which trjcat has shown the warning while joining.<br>
So what should i do?<br><br>Thanks,<br><br>Anirban<br><br><div class="gmail_quote">On Thu, May 5, 2011 at 7:58 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>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello Justin,<br>
<br>
Thanks for the reply.<br>
gmxcheck on the first trajectory shows:<br>
<br>
-------------------------------------------------------------------------------------------------<br>
Checking file protein_3000NS_2.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 2957280.000 # Atoms 57296<br>
Reading frame 1400 time 2999280.000 <br>
Item #frames Timestep (ps)<br>
Step 1425 30<br>
Time 1425 30<br>
Lambda 1425 30<br>
Coords 1425 30<br>
Velocities 1425 30<br>
Forces 0<br>
Box 1425 30<br>
---------------------------------------------------------------------------------------------------<br>
<br>
And on the second trajectory shows:<br>
<br>
---------------------------------------------------------------------------------------------------<br>
Checking file B2AR_self_assembly_3500NS.trr<br>
trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 3000000.000 # Atoms 57296<br>
Reading frame 16000 time 3480000.000 <br>
Item #frames Timestep (ps)<br>
Step 16667 30<br>
Time 16667 30<br>
Lambda 16667 30<br>
Coords 16667 30<br>
Velocities 16667 30<br>
Forces 0<br>
Box 16667 30<br>
---------------------------------------------------------------------------------------------------<br>
<br>
So gmxcheck does not show any warning/error.<br>
Then why I am getting the warning from trjcat. And how to remove it?<br>
<br>
</blockquote>
<br></div></div>
I don't know yet. A few more questions:<br>
<br>
1. What version of Gromacs are you using?<br>
<br>
2. How many total trajectories are you concatenating? You said there was a problem from 10 -> 3000000 ns, but I don't see any times shown here below 2957280. The real problem could be early on in the trajectory.<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;">
Thanks,<br>
<br>
Anirban<div><div></div><div class="h5"><br>
<br>
On Thu, May 5, 2011 at 7:19 PM, 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>>> wrote:<br>
<br>
<br>
<br>
Anirban Ghosh wrote:<br>
<br>
<br>
Hi ALL,<br>
<br>
I am trying to use trjcat -f input files -o output_file to join<br>
to very larger trajectories. However I am getting the following<br>
error:<br>
<br>
-------------------------------------------------------------------------------------------------------------------------------------------<br>
Continue writing frames from protein_3000NS_2.trr t=2.95728e+06<br>
ps, frame=98576 -> frame 100000 time 3000000.000 ps -><br>
frame 99980 time 2999400.000 ps WARNING: Frames around<br>
t=3000000.000000 ps have a different spacing than the rest,<br>
might be a gap or overlap that couldn't be corrected automatically.<br>
Reading frame 0 time 3999990.000 lasttime 3e+06<br>
<br>
Continue writing frames from protein_4000NS.trr t=3.99999e+06<br>
ps, frame=100001 -------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
And if I use this resultant output trajectory for further<br>
analysis like g_sas, then a portion between around 10 ns and<br>
3000000 ns is simply joined by a straight line.<br>
How to remove this inconsistency from the two trajectories?<br>
Any suggestion is welcome.<br>
<br>
<br>
What does gmxcheck tell you about each of the individual<br>
trajectories (prior to running trjcat)?<br>
<br>
-Justin<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></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>
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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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