[gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

[Nilesh Dhumal]

Thanks for you reply.

I am doing simulation for ionic liquids BMIM + CL. Total number of atoms
are 3328.

Nilesh

> Assuming you're using LINCS, from the manual:
> "With domain decomposition, the cell size is limited by the distance
> spanned by *lincs-order*+1 constraints."
> Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance
> for
> 5 bonds.
>
> Which means that you're probably using too many nodes for the size of your
> system.
>
> Hope that helps. If it doesn't you'll need to provide some information
> about your system.
>
> -Trayder
>
>
>
> On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal
> <ndhumal at andrew.cmu.edu>wrote:
>
>> Hello,
>>
>> I am getting the following error for simulation. I am using Gromacs
>> VERSION 4.5.5 and running on 24 processors.
>>
>> Should I reduce the number of processor or the problem is in bonded
>> parameters. If I use -nt 1 option. I could run the simulation.
>>
>> Fatal error:
>> There is no domain decomposition for 16 nodes that is compatible with
>> the
>> given box and a minimum cell size of 0.826223 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>> Look in the log file for details on the domain decomposition
>>
>>
>> Nilesh
>>
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