[gmx-users] Regarding error.

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 12:15:43 CEST 2012

On 6/11/12 4:37 AM, Seera Suryanarayana wrote:
> Dear Justin sir,
>                       I am simulating a protein 1AKI.pdb which is example of
> your tutorial.I am doing simulations as your tutorial.I didnt get any errors
> upto the commond "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o
> em.tpr".After this as your tutorial i used the commond " mdrun -v -deffnm em",
> then i got the following error.
> Fatal error:
> Domain decomposition does not support simple neighbor searching, use grid
> searching or use particle decomposition
> Kindly tell me how to overcome this error.

Mark has already addressed this issue:


You will either need to make a suitable change to the .mdp file or to the mdrun 
command line, both of which are suggested in the error message.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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