# Simulation breaks the side chain of some residue gromacs

**URL:** <https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331>\
**Category:** User discussions\
**Tags:** mdrun, analysis-tools\
**Created:** [February 13, 2024, 7:13pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331 "2024-02-13T19:13:47Z")\
**Posts on this page:** 1\
**Showing post:** 2

<div class="post-metadata">

**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [February 13, 2024, 7:32pm UTC](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331/2 "2024-02-13T19:32:03Z")

</div>

The visualization don’t necessarily represent the topology since it only uses distance-based heuristics to place bonds when atoms are close enough ([Bond Dissappearing in VMD - #2 by rpsingh](https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009/2)), so weird artefacts like this often appear. As long as the topology file is correct, your simulation should be correct (Gromacs can’t add or remove bonds during the simulation)

---

_[View the full topic](https://gromacs.bioexcel.eu/t/simulation-breaks-the-side-chain-of-some-residue-gromacs/8331)._