On 8/21/19 12:30 PM, Dhrubajyoti Maji wrote:
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.
Use fewer processors. You can't arbitrarily split any system over a
given number of processors. Prior runs may have worked if, for instance,
box dimensions were different, but now you have to adjust.
-Justin
Thanks and regards.
Dhrubajyoti Maji
On Wed, 21 Aug 2019 at 16:21, Justin Lemkul <jalem...@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
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Justin A. Lemkul, Ph.D.
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Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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==================================================
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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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