Opinion about RMSD curve

User discussions
1

GROMACS version: 2020.2
GROMACS modification: Yes/No
Dear Gromacs User,
I ran a 100ns simulation and calculated rmsd using energy minimized structure as a reference. Curve is attached below. as its not typical hyperbolic curve, I have a doubt about it. I am new to simulation but I think rmsd curve should be hyperbolic shape ie initial increment and plateau after sometime. During the initial cycles of simulation, rmsd will change more and will become stable when the system is relaxed. So i am asking for your opinion about the rmsd curve below. Is it normal or something wrong with my simulation?

Thank you
Best Regards
Veeru

Test
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2

There’s very little one can tell from an RMSD curve. Yours appears to be leveling off in general but maybe there’s some flexible region of the structure that is simply oscillating a lot. If you have a lot of loops, you can exclude them from the calculation to see if the core tertiary structure is stable, but again, there is very little one can conclude from RMSD anyway.