Unstable RMSD Fluctuations in Protein Simulation: Potential Issues?

User discussions
1

GROMACS version: gromacs-2022.2

"Hello everyone,

I’m seeking some guidance on interpreting the attached RMSD plot of a molecular dynamics simulation for a protein backbone after fitting into the backbone itself. The plot shows fluctuations in RMSD over a 200 ns simulation, with notable instability and large deviations starting around 80 ns (Uploading the plot along). RMSD values range between 1 nm and 7 nm, with periods of high variability.

I wonder if this behavior is normal for such a simulation or if it could indicate a technical issue with the setup, simulation parameters, or system stability. Any insights on possible causes and suggestions for improving the analysis would be greatly appreciated.

Thank you!"

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2

It looks like it’s just a matter of periodic boundary conditions. Have you tried gmx trjconv -pbc nojump before analysing the trajectory?

3

You might need to first do a conversion with gmx trjconv -pbc mol before gmx trjconv -pbc nojump.

4

Will Definitely try this. Thank you.
I have done - gmx trjconv -pbc mol, will try the nojump command.