GROMACS version: 2020.2
GROMACS modification: No
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Has anyone encountered simulations where the RMSD of the protein backbone is between 3.5 and 4.0 nm?
I’ve recently performed 3 150-ns MD simulations on 3 separate dimers of the enolase superfamily; two were the same protein but one had two mutated residues, and the other was a homologous dimer. After analyzing the RMSD of the backbone for each dimer, I found that the homologous dimer had an RMSD around 0.2 nm, while the other two had RMSD that was between 3.5 and 4.0 nm. I have attached a picture showing the graphs of all three simulations at the end of this post.
Does this mean that the simulations with RMSD values closer to 4.0 nm unstable? Why would it be so much higher compared to the RMSD for the homologous protein with a very similar sequence and structure?