System and Structure Stability check before starting the analysis

[M_Abdelaal]

GROMACS version: 2020.2
GROMACS modification: No

Hello everybody,

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 ?

Many Thanks

[Dr_DBW]

My general advice would be that you check to ensure it has run long enough such that the property you are interested in has stabilised sufficiently to reach some equilibrium. If that property is still changing, then you have not run it long enough.

Re RMSD - https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions