GROMACS version: 2021.1
GROMACS modification: No
After finishing 300-ns production mdrun, the RMSD (ref: equilibrated) stabilizing at ~ 1.1 nm as shown below:
Is 1.1 nm is a normal range for my mutated protein? When I search the RMSD range in google and find that mostly the RMSD is less than 1 nm, so I am not sure if my RMSD is OK to use?
Also, for comparison, the wilde-type protein give the RMSD of ~ 0.8 nm, and the shape of “down direct half-circle” looks a little wired for me (I expect it to be stable). Also, at the end time of the simulation, the RMSD falls down suddenly to ~0.6 nm. Do you give some suggestions about this figure? Is it normal to use following structural analysis? Or I need more time to do simulation (but I think 300-ns is already long enough)?