# Choosing an appropriate RMSD cut off for gromos clustering

**URL:** <https://gromacs.bioexcel.eu/t/choosing-an-appropriate-rmsd-cut-off-for-gromos-clustering/3493>\
**Category:** User discussions\
**Created:** [January 17, 2022, 10:38pm UTC](https://gromacs.bioexcel.eu/t/choosing-an-appropriate-rmsd-cut-off-for-gromos-clustering/3493 "2022-01-17T22:38:36Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![s.walsworth](https://avatars.discourse-cdn.com/v4/letter/s/ba9def/32.png) [@s.walsworth](https://gromacs.bioexcel.eu/u/s.walsworth)\
**Post date:** [January 17, 2022, 10:38pm UTC](https://gromacs.bioexcel.eu/t/choosing-an-appropriate-rmsd-cut-off-for-gromos-clustering/3493/1 "2022-01-17T22:38:36Z")

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GROMACS version: 2020.4  
GROMACS modification: No

Hi all,

I’ve seen examples of people using the gromos clustering method whereby they use a varying RMSD cut off value to create a cluster that represents over half the conformations in a trajectory. Essentially I don’t know what the best approach to choosing the RMSD cut off value is. Is it to use the tightest/smallest RMSD cut off that still yields a cluster with \>50% conformations?

I’ve clustered using progressively tighter RMSD values whilst still having more than 50% and the central structures are identical, which makes me think this is probably a good way to approach this.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [January 18, 2022, 4:23am UTC](https://gromacs.bioexcel.eu/t/choosing-an-appropriate-rmsd-cut-off-for-gromos-clustering/3493/2 "2022-01-18T04:23:09Z")

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Isn’t this sort of the opposite of what clustering is intended to do? If you predetermine that you want 50% of the frames in a cluster, you can rig some value to give you that, but is the cluster truly a representation of similar structures, or is it a convenient outcome? In any case, the RMSD cutoff depends on the system; one would use a very different value for a globular protein with stable tertiary structure than what would be appropriate for an IDP.

There are better methods available than the GROMOS clustering method; there are shortcomings to this approach. It may be better to pursue those if it is not clear how to treat your system.

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**Author:** ![s.walsworth](https://avatars.discourse-cdn.com/v4/letter/s/ba9def/32.png) [@s.walsworth](https://gromacs.bioexcel.eu/u/s.walsworth)\
**Post date:** [January 18, 2022, 1:57pm UTC](https://gromacs.bioexcel.eu/t/choosing-an-appropriate-rmsd-cut-off-for-gromos-clustering/3493/3 "2022-01-18T13:57:02Z")

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I see what you’re getting at. Maybe an alternative whilst continuing with gromos would be to use the average RMSD as a cutoff.

I will read around other clustering methods, I only used gromos initially since I came across it in literature.