[gmx-users] RMSD plots protein-protein complex

[Dr. Seema Mishra]

I am also interested in answers to this thread. Can a protein only plot in a protein-peptide complex have increasing backbone RMSD values at 100 ns of simulations? If no, what needs to be done to stabilize trajectory?


--------------------------------------------
On Sun, 20/1/19, Justin Lemkul <jalemkul at vt.edu> wrote:

 Subject: Re: [gmx-users] RMSD plots protein-protein complex
 To: gmx-users at gromacs.org
 Date: Sunday, 20 January, 2019, 8:05 PM
 
 
 
 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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