# How to define backbone group in RNA **URL:** \ **Category:** User discussions\ **Created:** [December 20, 2020, 8:55am UTC](https://gromacs.bioexcel.eu/t/how-to-define-backbone-group-in-rna/1294 "2020-12-20T08:55:57Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![shailesh](https://avatars.discourse-cdn.com/v4/letter/s/50afbb/32.png) [@shailesh](https://gromacs.bioexcel.eu/u/shailesh)\ **Post date:** [December 20, 2020, 8:55am UTC](https://gromacs.bioexcel.eu/t/how-to-define-backbone-group-in-rna/1294/1 "2020-12-20T08:55:58Z")
GROMACS version: 20.3 GROMACS modification: No Here post your question I am currently performing a molecular dynamic simulation on RNA. while performing analysis of (FOR EXAMPLE RMSD) , during command execution i am not finding any option of selecting BACKBONE GROUP as in case of protein analysis. please suggest me as to what should I perform to obtain backbone group. if in case there isn’t an option of selecting backbone group in RNA analysis then what should be done to obtain similar results. Thanks and Regards Shailesh Mani Tripathi Central University of Rajasthan, Rajasthan India Email- [2019mppc005@gmail.com](mailto:2019mppc005@gmail.com) ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [December 21, 2020, 8:07am UTC](https://gromacs.bioexcel.eu/t/how-to-define-backbone-group-in-rna/1294/2 "2020-12-21T08:07:07Z")
Hi, You can generate an index file (ndx file), where you define a group containing the backbone atoms of RNA. Then you can give this index file as input to other gmx tools using the option -n {filename}.ndx To generate an index file for the backbone atom, you can use gmx make\_ndx > **[gmx make\_ndx — GROMACS 2020.4 documentation](http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html)** Best regards Alessandra