[gmx-users] MD run error

[Mark Abraham]

Hi,

What are you simulating, with what model physics?

Mark

On Mon, 19 Jun 2017 21:13 Mishelle Oña <samimishu at hotmail.com> wrote:

> Hi,
>
> I got this error. Can anyone explain me what it means.
>
> WARNING: This run will generate roughly 10571 Mb of data
>
> starting mdrun 'UNITED ATOM STRUCTURE FOR MOLECULE LIG in water'
> 10000000 steps,  20000.0 ps.
>
> NOTE: Turning on dynamic load balancing
>
>
> DD cell 3 0 0: Neighboring cells do not have atoms: 30
>
> DD cell 5 0 0: Neighboring cells do not have atoms: 41
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.5
> Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_con.c,
> line: 722
>
> Fatal error:
> DD cell 3 0 0 could only obtain 16 of the 17 atoms that are connected via
> constraints from the neighboring cells. This probably means your constraint
> lengths are too long compared to the domain decomposition cell size.
> Decrease the number of domain decomposition grid cells or lincs-order or
> use the -rcon option of mdrun.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Mishelle
>
>
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