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Hi all, I have seen others published RMSD graph on their simulations and what I can interpret is that the RMSD graph should have mild fluctuations to indicate that the protein is stable.
However, after analysing the RMSD graph from my simulations, I guessed I could interpret that my protein-protein complex is not stable. So, does this means the protein-protein complex cannot happen in real-life situations?
All you can really interpret from a large RMSD is that the conformation of the protein differs from its starting conformation, not necessarily that such changes are unrealistic. I would suggest visualizing the protein to see what’s causing these fluctuations
Hey nurarshad
The RMSD graph seems unstable, but you can make things work.
You can attempt another MD simulation, but this time, consider a longer NPT equilibration period. Once equilibrated, verify the pressure constant of the resulting complex.
gmx energy -f npt -o pressure.xvg
Positive pressure supports less RMSD fluctuation; if things are still not working, you need to re-parametrize the ligand with a different force field or go with a longer run so that after 150 ns you can expect a stable trajectory.
