[gmx-users] domain decomposition error

[Tsjerk Wassenaar]

Hi SMA,

It says you have bonds over large distances. Check the
structure/topology/setup.

Cheers,

Tsjerk
On Oct 27, 2015 08:02, "Musharaf Ali" <skmali786 at gmail.com> wrote:

> Dear users
> During energy minimization for IL-water system in a box size of 4.7x4.7x9.4
> with432 BMIMTF2N and 3519 water molecules, the following error is written
> in the md.log file.
>
> Initializing Domain Decomposition on 144 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 9.371 nm, LJ-14, atoms 622 624
>   multi-body bonded interactions: 9.371 nm, Angle, atoms 620 622
> Minimum cell size due to bonded interactions: 10.308 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
> Estimated maximum distance required for P-LINCS: 0.218 nm
> Guess for relative PME load: 0.15
> Will use 120 particle-particle and 24 PME only nodes
> This is a guess, check the performance at the end of the log file
> Using 24 separate PME nodes, as guessed by mdrun
> Optimizing the DD grid for 120 cells with a minimum initial size of 10.308
> nm
> The maximum allowed number of cells is: X 0 Y 0 Z 0
>
> -------------------------------------------------------
> Program mdrun_mpi_d, VERSION 4.6.1
> Source code file: /root/GROMACS-GPU/gromacs-4.6.1/src/mdlib/domdec.c, line:
> 6775
>
> Fatal error:
> There is no domain decomposition for 120 nodes that is compatible with the
> given box and a minimum cell size of 10.3078 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Could you please suggest how to get rid off it.
>
> Thanks in advance
>
> SMA
> --
> 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-request at gromacs.org.
>