[gmx-users] trr and xtc
jamie.seyed at gmail.com
Wed Jul 22 17:49:56 CEST 2009
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
On Wed, Jul 22, 2009 at 11:32 AM, Justin A. Lemkul <jalemkul at vt.edu> 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 :)
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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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