GROMACS version: 2023
GROMACS modification: Yes/No
What does this constant line indicate?
It would help to visualize the system, it’s hard to say what’s going on from the RMSD graph alone, are you familiar with using VMD to do so?
no actually, however I’ve performed other post simulation assessments
You can use VMD to either visualize the trajectory, or you could take snapshots of the trajectory at specific times using gmx trjconv (using the -dump flag) and visualize the system with either VMD or PyMOL to see what’s going on
This seems to be an error in the data file you are plotting. Take a look a the file itself with a text editor, you will probably see values for x (time) and y (RMSD) up to x = 1000 ps and then a last point at t = 2000 without anything else in between which probably indicates some problem in the generation itself of the data file you are printing!