Hi Mark and Justin, I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie (60nm) side.
I tried using only two nodes, it gives the same error There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 0.889862 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Amit On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > ----- Original Message ----- > From: "Justin A. Lemkul" <jalem...@vt.edu> > Date: Saturday, February 20, 2010 10:13 > Subject: Re: [gmx-users] domain decomposition and load balancing > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > > > > Amit Choubey wrote: > > >Hi Mark, > > > > > >I am not using PME calculation. > > > > > >I was hoping mdrun will do the cell allocation itself. > > > > > > > It will, unless it can't, which is exactly your problem. > > Mark's point stands, regardless of whether or not you're using > > PME. DD requires certain minimum size requirements (which > > are discussed in the manual and the Gromacs 4 paper), so you > > have two choices: > > > > 1. Read about the options mdrun is telling you about. > > 2. Use fewer nodes so that the DD algorithm can construct > > reasonably-sized domains. > > 3. Use a larger simulation system so the minimum cell size is larger w.r.t. > the cutoffs > 4. (If reasonable) Don't use pbc=xy > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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