[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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>> -- ========================================
>>
>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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