Well, I do not do anything special when preparing this system compared to other systems that do not show this issue.
I have carefuly inspected my system and I know what is wrong. I did some manipulations to PDB file due to missing fragment of residue and accidentally put NZ atom of Lysine like 3.5 nm from the side-chain carbon... Sorry for bothering. Best wishes, Dawid 2018-04-15 16:41 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > 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. > -- 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.