[gmx-users] Domain decomposition error

Justin Lemkul jalemkul at vt.edu
Sun Apr 15 16:42:07 CEST 2018

On 4/15/18 9:29 AM, Dawid das wrote:
> Dear Gromacs Users,
> I run numerous MD simulations for similar systems of protein in water box
> and
> for only one system I encounter error:
> *Fatal error:There is no domain decomposition for 4 ranks that is
> compatible with the givenbox and a minimum cell size of 3.54253 nmChange
> the number of ranks or mdrun option -rddLook in the log file for details on
> the domain decomposition*
> I found explanation of this error in Gromacs documentation as well as on
> the mailing
> list, however I still do not understand why I get this only for one system
> out of many.
> There is nothing special about it, I mean its size for instance is similar
> to this of
> others systems.
> What can be source of this error, then? Can it be the system size or
> placement of
> charge groups?

A "normal" protein-in-water system will never have such a minimum cell 
size unless you're doing something unconventional, like long-distance 
restraints, free energy calculation adding explicit intramolecular 
exclusions, or some weird topology element that is not conventional. If 
you can give more details (and the information from the .log file about 
how DD is determining this minimum cell size), we can probably say more.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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