[gmx-users] error when running NVT equilibrium

[Justin Lemkul]

On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
> After doing step 6 (Do a short energy minimization and position restrained
> simulation),i carry out running NVT equilibrium. But it appears the error
> in the terminal :
>
> Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 5.2375 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
> Look in the log file for details on the domain decomposition
>
> What can i do to fix this error ?
>

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 fact that the minimum size is over 5 nm is very odd.  Are there very 
long-range bonded interactions of some sort?  Normally the minimum box size is 
very close to the value of the longest cutoff unless something abnormal is present.

-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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