Interpreting GROMACS results (RMSD plot)

[nurarshad]

GROMACS version: 2023.4
GROMACS modification: No
Hi everyone, I am new to GROMACS and I have been following the Lysozyme in Water tutorial to simulate my docked protein-protein complex generated from ClusPro to check for the structural stability and flexibility of the docked complex. However, after running a 120ns simulation, my RMSD plot for my complex does not show that the docked complex was stable since the value is within the range between 1.5-2nm, and the other complex was between 2.75-3.05nm.

FYI, both of my simulations were cut before the simulations were complete due to power down and to continue the simulations I extend it to another 20ns (my initial running time was 100ns), which is why my total simulation time was 120 ns.

I have attached the plot for my RMSD values of both complexes. I hope someone here can help me interpret the results for my docked complexes. Thank you in advanced!

[asif2]

So why do these two RMSD trajectories look different? Are they the same protein or two different proteins?

Generally, a deviation of 2 Å is considered good. but in your condition, it’s doubled.

[Note: 0.1 nm = 1Å]

Still, if the trajectory converges at 2 nm deviation, it can be considered stable, but your RMSD graph doesn’t show any linearity. Therefore, we can conclude that the trajectory is unstable.

as you stated you are new to MD simulation

did you performed trajectory correction prior to the RMSD analysis ??