Re: [gmx-users] trr and xtc

[Justin A. Lemkul]

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.

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 <jalem...@vt.edu 
<mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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

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