[gmx-users] RMSD plots protein-protein complex

[Justin Lemkul]

On 1/18/19 11:55 AM, marzieh gharouni wrote:
> 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.

The images mean nothing in the absence of your exact commands and 
evidence of the groups you selected for analysis (copy and paste all 
this directly from your terminal).

-Justin

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Justin A. Lemkul, Ph.D.
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