[gmx-users] trr and xtc

[Jamie Seyed]

Hi Justin,
nstxout=0
nstvout=0

Pcoupl=berendsen
Pcoupltype=isotropic

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 <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 :)
>
> -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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