GROMACS version: 2020.2
GROMACS modification: No
I am simulating the deposition of C60 Molecules onto a graphene sheet. I finished the simulation (energy minimization then nvt then npt then md run) successfully.
Is there any check I can do to make sure that my system is ready to start the analysis (I am interested in measuring the density using gmx density) ?
In Dr. Justin tutorials, he started the analysis with the structure stability, I did the same and I have attached the graph showing the RMSD relative to the structure present in the minimized equilibrated system -Drawn in purple and the RMSD relative to the crystal structure - Drawn in yellow)
There is a difference between the 2 graphs (relative to the minimized structure and relative to the crystal structure) is that normal ?
What are the numbers on the y-axis (RMSD nm) refer to and how to judge if the values are logic or not (since I got values up to 5 nm while in the protein tutorial the values was 0.1 nm)?
I have noticed that starting from 1.5 ns both curves started to be steady, does this mean that my system is stable ?