[gmx-users] trr and xtc

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 22 17:32:54 CEST 2009

Jamie Seyed wrote:
> Dear all,
> I did a simulation of spce water and every thing seemed ok, when I did 
> mdrun -s file.tpr -o file.trr -c file_out.gro -v -g file.log, I got a 
> file.trr with zero size, but I have file.xtc that seems fine with VMD. I 
> don't what happened here. Any idea?

What did you set as nstxout and nstvout?  Depending on what you set for these 
parameters, you may not get much in the .trr file; the final frame should have 
been written, however.  Maybe something went wrong with the filesystem (a blip), 
and the output was suppressed.  I've had that happen when a simulation is 
finishing and a .gro file is written, but has nothing in it.

> Also I looked at the box size from first file.gro and last 
> file_out.gro..... It shows the box size has been changed a little bit:
> first it was 1.86206 1.86206  1.86206
> finally it is 1.86586  1.86586  1.86586

What kind of pressure coupling are you using (if any)?

> Can someone please kindly make it clear to me why it happened?

In general, posting the text of your .mdp file is a good idea.  That way, the 
answers to my questions above are answered :)


> Thanks,
> Jamie
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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