[gmx-users] trr and xtc

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto: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 <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

========================================