RMSD Calculation of Protein (have 2 chains-heterodimer)

GROMACS version: 2020.1.1
GROMACS modification: Yes/No
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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.

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.


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@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.

Thank you for your suggestion.

Thanks, happy to hear your solution soon.

Couldn’t get it to work. I am considering extending the simulation. My results show high RMSD at 100 ns.