# There were 2136 inconsistent shifts. check your topology?

**URL:** <https://gromacs.bioexcel.eu/t/there-were-2136-inconsistent-shifts-check-your-topology/10540>\
**Category:** User discussions\
**Created:** [November 13, 2024, 11:38am UTC](https://gromacs.bioexcel.eu/t/there-were-2136-inconsistent-shifts-check-your-topology/10540 "2024-11-13T11:38:04Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [November 13, 2024, 11:38am UTC](https://gromacs.bioexcel.eu/t/there-were-2136-inconsistent-shifts-check-your-topology/10540/1 "2024-11-13T11:38:04Z")

</div>

GROMACS version: 2022

Dear Gromacs users,

I am studying the diffusion of water in MFI zeolite. The simulation is done without any errors. However, When I want to calculate the diffusion coefficient of water using `gmx msd` I see this message on the terminal screen:

```auto
there were 2136 inconsistent shifts. check your topology.

```

The Structure is periodic and I have applied PBC in three directions. I get a linear MSD and diffusion coefficient as output. However, my concern is that this diffusion coefficient is not reliable. What is the problem? Is there any consideration for such systems?  
I also added `periodic-molecule = yes` to the .mdp file. But still, the inconsistent shift exists.

Thanks for your help