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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.