Jamie Seyed wrote:
Hi Justin,
nstxout=0
nstvout=0
Right, then the .trr file should be empty until the very end, when the last
frame should be written. Like I said, probably a filesystem blip.
Pcoupl=berendsen
Pcoupltype=isotropic
Note that all of your box vectors are the same at the end. This is probably a
consequence of isotropic pressure coupling.
-Justin
In fact I used the mdp file of /tuto/water and I modified it for PME and
v-rescale. But the rest is the same (I am using version 4.0.5)
I finished the simulation but I saw file.trr is empty... the rest seems
fine...even file.xtc
Thank you,
Jamie
On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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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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