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.
It depends what you want:
- the RMSD of one chain after fitting all backbone atoms (both chains)
- 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.
@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.