# Is it norm with RMSD stabilizing at ~1.1 nm when finishing production mdrun?

**URL:** <https://gromacs.bioexcel.eu/t/is-it-norm-with-rmsd-stabilizing-at-1-1-nm-when-finishing-production-mdrun/1844>\
**Category:** User discussions\
**Created:** [March 28, 2021, 2:13pm UTC](https://gromacs.bioexcel.eu/t/is-it-norm-with-rmsd-stabilizing-at-1-1-nm-when-finishing-production-mdrun/1844 "2021-03-28T14:13:08Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![minghao2121](https://avatars.discourse-cdn.com/v4/letter/m/c67d28/32.png) [@minghao2121](https://gromacs.bioexcel.eu/u/minghao2121)\
**Post date:** [March 28, 2021, 2:13pm UTC](https://gromacs.bioexcel.eu/t/is-it-norm-with-rmsd-stabilizing-at-1-1-nm-when-finishing-production-mdrun/1844/1 "2021-03-28T14:13:08Z")

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GROMACS version: 2021.1  
GROMACS modification: No  
Hello,  
After finishing 300-ns production mdrun, the RMSD (ref: equilibrated) stabilizing at ~ 1.1 nm as shown below:  
 ![rmsd_1.1nm_MUT_2021-03-28_095621](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/d9e2b29d9f286e5faa96edb70a95adab4b6a8e7c.png)

Is 1.1 nm is a normal range for my mutated protein? When I search the RMSD range in google and find that mostly the RMSD is less than 1 nm, so I am not sure if my RMSD is OK to use?

Also, for comparison, the wilde-type protein give the RMSD of ~ 0.8 nm, and the shape of “down direct half-circle” looks a little wired for me (I expect it to be stable). Also, at the end time of the simulation, the RMSD falls down suddenly to ~0.6 nm. Do you give some suggestions about this figure? Is it normal to use following structural analysis? Or I need more time to do simulation (but I think 300-ns is already long enough)?

![rmsd_0.8 nm_WT_2021-03-28_100834](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/0b6faff10ec96a0914ab5bc309cb7fa3a79d2d39.png)

Thanks,  
Ming

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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:** [March 29, 2021, 8:05pm UTC](https://gromacs.bioexcel.eu/t/is-it-norm-with-rmsd-stabilizing-at-1-1-nm-when-finishing-production-mdrun/1844/2 "2021-03-29T20:05:37Z")

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RMSD is an extrinsic property so there are no rules about what it should be. If you have flexible regions or termini, the value can be artificially inflated.

Bottom line: RMSD tells you very little, if anything, that is useful.

Analyze other structural quantities of interest to see if they are sufficiently converged.

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<div class="post-metadata">

**Author:** ![minghao2121](https://avatars.discourse-cdn.com/v4/letter/m/c67d28/32.png) [@minghao2121](https://gromacs.bioexcel.eu/u/minghao2121)\
**Post date:** [March 29, 2021, 8:27pm UTC](https://gromacs.bioexcel.eu/t/is-it-norm-with-rmsd-stabilizing-at-1-1-nm-when-finishing-production-mdrun/1844/3 "2021-03-29T20:27:14Z")

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Thanks, Justin. Sure, my protein has a flexible CTD. I will check other metrics.  
Best,  
Ming