[gmx-users] Domain decomposition error while running coarse grained simulations on cluster

[Justin Lemkul]

On 9/1/19 5:44 AM, Avijeet Kulshrestha wrote:
> Hi all,
> I am running martini coarse-grained simulation with 15 fs of time step in
> gromacs 2018.6. I have 25859 number of atoms and my box size is:
> 12.00000  14.00000  18.00000
> Where I have Protein, membrane (DPPC) and ions.
> I have minimized energy with 16 processor and -rdd option as 2.5. It worked
> fine but later in NVT simulation, this started giving errors.
> *I am getting the following error without -rdd option when I used 1 node
> and 8 processor per node:*
> Fatal error:
> There is no domain decomposition for 8 ranks that is compatible with the
> given
> box and a minimum cell size of 7.69783 nm

This minimum cell size is significantly larger than a normal simulation 
would require. Do you have restraints or other non-standard interactions 
defined? The .log file snippet that describes the DD setup would be 
useful for tracking the issue down.

-Justin

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Justin A. Lemkul, Ph.D.
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