[gmx-users] RMSD plots protein-protein complex

[marzieh gharouni]

Hello
I did a simulation of protein-protein interaction with Gromacs code. In
this simulation, the number of amino acids in each protein is about 230.
The simulation production run was 300ns. After analyzing trajectory, I
found that RMSD value of protein-protein complex fluctuated near 1.8 nm but
the single of each protein has RMSD plots around 0.35 nm. Other plots (rg ,
rmsf) of the protein-protein complex show my complex system is stable. But
I have a problem with the RMSD value (not behavior) of mix proteins. Is it
normal?
Please see share files
Rmsd of protein A-Protein B complex:
https://drive.google.com/file/d/16BoOdfUev2Bh7zgUCj4pOBAyPQLS_EJY/view?usp=sharing
Rmsd of Protein A:
https://drive.google.com/file/d/1QYt2rQQuNK4qqwp9O-k40uglSZaEYjAe/view?usp=sharing
Rmsd of protein B:
https://drive.google.com/file/d/1DYJ_jIUf-E9I8M38MrBxdh1tAtaIsBod/view?usp=sharing
Thanks in advance.