# periodic boundaries in a molecule type

**URL:** <https://gromacs.bioexcel.eu/t/periodic-boundaries-in-a-molecule-type/1807>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [March 24, 2021, 9:01am UTC](https://gromacs.bioexcel.eu/t/periodic-boundaries-in-a-molecule-type/1807 "2021-03-24T09:01:50Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![boufissiou](https://avatars.discourse-cdn.com/v4/letter/b/5f8ce5/32.png) [@boufissiou](https://gromacs.bioexcel.eu/u/boufissiou)\
**Post date:** [March 24, 2021, 9:01am UTC](https://gromacs.bioexcel.eu/t/periodic-boundaries-in-a-molecule-type/1807/1 "2021-03-24T09:01:50Z")

</div>

i faced this problem while doing the simulation by gromacs  
Program: gmx mdrun, version 2020  
Source file: src/gromacs/pbcutil/mshift.cpp (line 904)

Fatal error:  
There are inconsistent shifts over periodic boundaries in a molecule type  
consisting of 52 atoms. The longest distance involved in such interactions is  
9.359 nm which is above half the box length. Either you have excessively large  
distances between atoms in bonded interactions or your system is exploding.

---

<div class="post-metadata">

**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [March 25, 2021, 10:20am UTC](https://gromacs.bioexcel.eu/t/periodic-boundaries-in-a-molecule-type/1807/2 "2021-03-25T10:20:47Z")

</div>

Hi,

you can use a visualization software to understand what happen to your system . This may allow you to understand where the problem is.

Best regards  
Alessandra