[gmx-users] trr and xtc

Jamie Seyed jamie.seyed at gmail.com
Wed Jul 22 23:57:08 CEST 2009


Hi,

On Wed, Jul 22, 2009 at 1:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jamie Seyed wrote:
>
>> Thank you Justin,
>>  But how I can prevent from that (filesystem blip) to happen. Also May I
>>
>
> I know nothing about your filesystem, but sometimes these things happen
> randomly.  Try re-running with nstxout at some value other than zero and see
> if you get a non-empty .trr file.


Yes, It is ok now. I re-run it  with nonzero nstxout ! Thanks for all
comments.


>  change Pcoupl= Parrinello-rahman instead of berendsen (has it any
>> effect?? since I have changed Tcoupl=v-rescale instead of berendsen)?
>>
>
> Haphazardly changing algorithms for T- and P-coupling without knowing why
> is a recipe for disaster.  Read the literature about each methodology, and
> choose the one that's appropriate.
>
> The "problem" regarding box dimensions you pointed out before is related to
> the fact that you are using isotropic pressure coupling, wherein the box
> dimensions scale uniformly.  That will be the case regardless of which
> algorithm you use. If the box dimensions change, that's just reality :)
>
> If for some reason you want to fix the box dimensions, use Pcoupl = no.
>
> 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.......??
>>
>>
>
> The .mdp file was generated using an old version of Gromacs.  Refer to the
> manual for changes, and delete that line from the .mdp file.
>
> -Justin
>
> Thanks,
>> Jamie
>>
>> On Wed, Jul 22, 2009 at 11:53 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>>         <mailto: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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>>
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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/> <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 <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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