[gmx-users] domain decomposition

[Dhrubajyoti Maji]

Many tanks Dr. Lemkul for your kind reply. I have checked the link. I have
done the equlibration step successfully but the error appears at production
run. The change is only that now I am writing the output trajectory. So, if
I had any problem in topology or mdp file then I think my equilibration
should have been failed. I am a newbie and I can't understand what exactly
is going wrong. Any kind of suggestion will be highly appreciated.
Thanks and regards.
Dhrubajyoti Maji


On Wed, 21 Aug 2019 at 16:21, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/21/19 1:00 AM, Dhrubajyoti Maji wrote:
> > Dear all,
> >      I am simulating a system consisting urea molecules. After
> successfully
> > generating tpr file while I am trying to run mdrun, the following error
> is
> > appearing.
> > Fatal error:
> > There is no domain decomposition for 72 ranks that is compatible with the
> > given box and a minimum cell size of 0.5924 nm
> > Change the number of ranks or mdrun option -rcon or -dds or your LINCS
> > settings.
> > All bonds are constrained are by LINCS algorithm in my system and
> dimension
> > of my box is 3.40146 nm. I have checked gromacs site as well as mailing
> > list but couldn't understand what to do. Please help me with the issue.
>
>
> http://manual.gromacs.org/current/user-guide/run-time-errors.html#there-is-no-domain-decomposition-for-n-ranks-that-is-compatible-with-the-given-box-and-a-minimum-cell-size-of-x-nm
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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