[gmx-users] domain decomposition

[Mark Abraham]

On 4/04/2011 1:51 AM, mohsen ramezanpour wrote:
> Dear All
>
> I have a file which contains afew residues (noncontinuous),
> When I use mdrun on a computer(4 cpu) I am facing with the following 
> Error:
>
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with 
> the given box and a minimum cell size of 3.28697 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
>
>
> it is relating to domain decomposition,
> Besides I checked either restraining residues and not restraining.But 
> it dosn't differed
>
> I changed the number of nodes to 1 but it didn't work!
> mpirun   -np  1  mdrun   -v   -deffnm  EM
>
> Besides I looked in the log file and the important part of it was:
>
> Initializing Domain Decomposition on 4 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: 2.988 nm, LJ-14, atoms 922 943
>   multi-body bonded interactions: 2.988 nm, Proper Dih., atoms 922 943
> Minimum cell size due to bonded interactions: 3.287 nm
> Using 0 separate PME nodes
> Optimizing the DD grid for 4 cells with a minimum initial size of 3.287 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 1
>
>
> please let me know how can I solve this problem.
> Thanks in advance

Why do you have bonds nearly 3nm long?

Mark