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. -- Gromacs Users mailing list
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