[gmx-users] node decomposition' problem

[Justin A. Lemkul]

On 7/9/12 4:23 PM, Thales Kronenberger wrote:
> I'm trying to run a kinase (what means that I had ATP - large charged
> group) energy minimization and then MD.
>
> But when I put my protein together with its ligands I gotcha the
> follow error message:
>
> "There is no domain decomposition for 6 nodes that is compatible with
> the given box and a minimum cell size of 6.47943 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition"
>
> I read about in gromacs forums and I can force the thing's running
> with the option nt 1 (one node...).
>
> My problem is that I still want to run in parallel. Is it still that
> possible for my system or I'm doomed to the 1 core simulation
>

The minimum charge group size depends on a whole host of factors:

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

The large size you have obtained indicates there are likely problems with the 
.mdp file, topology, or both.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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