# Rms shooting for end amino acids

**URL:** <https://gromacs.bioexcel.eu/t/rms-shooting-for-end-amino-acids/248>\
**Category:** User discussions\
**Created:** [June 5, 2020, 1:53pm UTC](https://gromacs.bioexcel.eu/t/rms-shooting-for-end-amino-acids/248 "2020-06-05T13:53:09Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Yogeshb](https://avatars.discourse-cdn.com/v4/letter/y/bc79bd/32.png) [@Yogeshb](https://gromacs.bioexcel.eu/u/Yogeshb)\
**Post date:** [June 5, 2020, 1:53pm UTC](https://gromacs.bioexcel.eu/t/rms-shooting-for-end-amino-acids/248/1 "2020-06-05T13:53:09Z")

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GROMACS version: Gromacs 2019.1  
GROMACS modification: No  
Hello users,  
Hello Justin,‬

‪Had some doubt about gmx rms command, I was calculating rmsd for individual amino acids of peptide, in my case the rmsd for tail amino acids is shooting 100 fold. Command is correct, I cross checked, I am making structure whole before running rms‬  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/47315f21ffe5001770c5344ab39c8c951e05a9d0.jpeg)

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<div class="post-metadata">

**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:** [June 5, 2020, 2:30pm UTC](https://gromacs.bioexcel.eu/t/rms-shooting-for-end-amino-acids/248/2 "2020-06-05T14:30:10Z")

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Termini are generally very flexible. Watch the trajectory to see how much these amino acids move during the simulation.