[gmx-users] no domain decomposition

[Mark Abraham]

Why do you have a bonded interaction whose length is 1.6nm? Mdrun is
telling you that is limiting you.

Mark
On Jun 25, 2014 12:26 PM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:

> Hello,
>
> I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
> my system. I am getting following error:
>
>
> Fatal error:
> There is no domain decomposition for 16 nodes that is compatible with the
> given box and a minimum cell size of 1.81239 nm
> Change the number of nodes or mdrun option -rdd
>
>  Following is an excerpt of log file:
>
> Initializing Domain Decomposition on 16 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 1.648 nm, Bond, atoms 2161 2163
>   multi-body bonded interactions: 1.648 nm, Angle, atoms 2161 2163
> Minimum cell size due to bonded interactions: 1.812 nm
> Using 0 separate PME nodes, as there are too few total
>  nodes for efficient splitting
> Optimizing the DD grid for 16 cells with a minimum initial size of 1.812 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 6
>
>
> *I tried decreasing number of nodes from 48 to 16, but this error appears
> always. 2161 and 2163 atoms mentioned in log file excerpt above are formate
> atoms each of which is in a different charge group. I can't put them in
> same charge group, since they are different energy groups as we can see. *
>
> *Any suggestions how to interpret log file excerpt or what more can be
> done?*
>
> Thanks
> Chetan
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