# Bond Dissappearing in VMD

**URL:** <https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [March 21, 2023, 5:41am UTC](https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009 "2023-03-21T05:41:14Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\
**Post date:** [March 22, 2023, 12:35pm UTC](https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009/2 "2023-03-22T12:35:07Z")

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The gro file has only coordinates and no bond linkage info. VMD uses a distance-based heuristics which means that two atoms within a given distance will be shown as bonded. You can see all tyles of artefacts based on this e.g., hydrogen bonded to 2 atoms! Don’t worry as long as the topology file is correct.

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_[View the full topic](https://gromacs.bioexcel.eu/t/bond-dissappearing-in-vmd/6009)._