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 :)
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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