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

--
==================================================

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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