# RMSD Calculation of Protein (have 2 chains-heterodimer) **URL:** \ **Category:** User discussions\ **Tags:** mdrun, analysis-tools\ **Created:** [September 28, 2022, 1:05am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893 "2022-09-28T01:05:40Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![nrfarhana](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@nrfarhana](https://gromacs.bioexcel.eu/u/nrfarhana)\ **Post date:** [September 28, 2022, 1:05am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/1 "2022-09-28T01:05:40Z")
GROMACS version: 2020.1.1 GROMACS modification: Yes/No Here post your question My protein has 2 chains (heterodimer) and I did an index file for each chain to analyze the rmsd value, respectively. I choose ‘17’ for both least squares fit and rmsd calculation for chain A (ns2b) as attached in the picture below. I am wondering whether I am doing the right method analysis. I try to choose group ‘4’ which is backbone for least square fit and ‘17’ for rmsd calculation but got unfamiliar rmsd graph pattern. ![photo1664326555](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/5/572358fed5924a39ea5ec10c401c677c09ce7792.jpeg) ![photo1664326555 (1)](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/0/08d8a60095959274f81b924685d6fb12c5d3de51.jpeg) ---
**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:** [September 28, 2022, 10:03am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/2 "2022-09-28T10:03:00Z")
Hi, It depends what you want: 1. the RMSD of one chain after fitting all backbone atoms (both chains) 2. the RMSD of one chain after fitting all chain atoms You can vizualize your trajectory to understand if the RMSD you got make sense. Maybe you need to post-process your trajectory using gmx trjconv. You can also have a look at previous posts on RMSD problems. \Alessandra ---
**Author:** ![rehoboam](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rehoboam/32/2566_2.png) [@rehoboam](https://gromacs.bioexcel.eu/u/rehoboam)\ **Post date:** [October 1, 2022, 4:01am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/3 "2022-10-01T04:01:03Z")
@nrfarhana I too am running a simulation for NS2B-NS3 protease and facing the same issue. Planning to use MDAnalysis package. I’ll drop a post here if I find a solution. ---
**Author:** ![nrfarhana](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@nrfarhana](https://gromacs.bioexcel.eu/u/nrfarhana)\ **Post date:** [October 2, 2022, 1:00am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/4 "2022-10-02T01:00:37Z")
Thank you for your suggestion. ---
**Author:** ![nrfarhana](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@nrfarhana](https://gromacs.bioexcel.eu/u/nrfarhana)\ **Post date:** [October 2, 2022, 1:05am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/5 "2022-10-02T01:05:54Z")
Thanks, happy to hear your solution soon. ---
**Author:** ![rehoboam](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rehoboam/32/2566_2.png) [@rehoboam](https://gromacs.bioexcel.eu/u/rehoboam)\ **Post date:** [October 5, 2022, 11:11am UTC](https://gromacs.bioexcel.eu/t/rmsd-calculation-of-protein-have-2-chains-heterodimer/4893/6 "2022-10-05T11:11:11Z")
Couldn’t get it to work. I am considering extending the simulation. My results show high RMSD at 100 ns.