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!
