[gmx-users] trr and xtc

[Jamie Seyed]

Thank you Justin,

But how I can prevent from that (filesystem blip) to happen. Also May I
change Pcoupl= Parrinello-rahman instead of berendsen (has it any effect??
since I have changed Tcoupl=v-rescale instead of berendsen)?
By the way there was a warning after doing grompp, it said "unknown or
double left-hand 'bd-temp' in parameter file"
In file.mdp it is
bd-temp=300
What about this warning related to the problem.......??

Thanks,
Jamie

On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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