[gmx-users] error when running NVT equilibrium

Justin Lemkul jalemkul at vt.edu
Mon Dec 17 14:56:16 CET 2012

On 12/17/12 8:53 AM, Kieu Thu Nguyen wrote:
> Dear All,
> I'm practising the tutorial 2a (protein in water) in the MARTINI tutorial.
> After doing step 6 (Do a short energy minimization and position restrained
> simulation),i carry out running NVT equilibrium. But it appears the error
> in the terminal :
> Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 5.2375 nm
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
> Look in the log file for details on the domain decomposition
> What can i do to fix this error ?


The fact that the minimum size is over 5 nm is very odd.  Are there very 
long-range bonded interactions of some sort?  Normally the minimum box size is 
very close to the value of the longest cutoff unless something abnormal is present.



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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