[gmx-users] Domain decomposition error
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
> 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users