[gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
trayder.thomas at monash.edu
Thu Oct 17 05:32:26 CEST 2013
Assuming you're using LINCS, from the manual:
"With domain decomposition, the cell size is limited by the distance
spanned by *lincs-order*+1 constraints."
Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for
Which means that you're probably using too many nodes for the size of your
Hope that helps. If it doesn't you'll need to provide some information
about your system.
On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal <ndhumal at andrew.cmu.edu>wrote:
> I am getting the following error for simulation. I am using Gromacs
> VERSION 4.5.5 and running on 24 processors.
> Should I reduce the number of processor or the problem is in bonded
> parameters. If I use -nt 1 option. I could run the simulation.
> Fatal error:
> There is no domain decomposition for 16 nodes that is compatible with the
> given box and a minimum cell size of 0.826223 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users