Dear Researchers,

I recently conducted Molecular Dynamics Simulations using GROMACS on a multimeric protein with an active site spanning portions of two chains, similar to the diazepam binding site in GABA-A receptor. Upon analysis, I encountered a challenge with the Root Mean Square Fluctuation (RMSF) plot, as the amino acid residue numbers from multiple chains overlapped, rendering the plot illegible.

In this scenario, what would be the best practice to effectively analyse and visualize the RMSF data?

I would greatly appreciate insights, suggestions, or any experiences from the community regarding strategies to address this issue.

Thank you for your expertise and contributions.

Best regards,

Md Emam Shikdar