# GROMACS RMSF Result Analysis Problem

This is RMSF for protein from GROMACS after 100ns simulation-

I have few questions-

1. Residue numbers are starting from 1650 to 1850, has it ignore LIG and HOH as residues?
2. There are three lines, so are there three chains and their residue number is same?
3. Are the straight lines connecting these chains or this is kind of loop something?
4. Since I am seeing 2nm or 20A fluctuation, is the protein quite disturbed?

3. The lines are merely an artefact. Those lines are the attempt of the engine to draw a single line for all the chains. You go from residue 1850 of chain 1 to residue 1650 of chain 2, and so on. Some tools handle this behaviour, others don't. I would suggest you to parse the PDB yourself and plot (e.g. ggplot) each chain as a layer of the same figures .