Strange RMSF Graphs

User discussions
1

GROMACS version: 2024
GROMACS modification: nNo
I recently performed the MD simulation for the docked structure (protein-protein) for a period of 100 ns . Upon trying to generate the RMSF graph I obtained strange lines (2) and would like somebody to help me rectify this. I used gnuplot for the graphs and when I opened my rmsf.xvg file I noticed that there were several instances of residue numbers being repeated which probably means my structure is a dimer/trimer (?) Is there anyway to make this graph uniform ? Also just to reconfirm if there is something wrong with my methodology I can also attach the other graphs I generated for the same run. Could you offer your expertise with respect to :-

  1. Accuracy of RMSD, SASA and Rg graphs
  2. Removing this connection or these additional lines over my RMSF graph
    rmsf_plot (1)
    rmsf_plot (1)800×600 59 KB

    [/grid]
2

rmsd_plot_ps
rmsd_plot_ps800×600 54.9 KB

3

sasa_plot
sasa_plot1280×960 103 KB

4

rg_plot
rg_plot1280×960 88.2 KB

5

You have multiple chains that use overlapping residue numbers. You will need to split the data into different data series or files to plot them as separate entities.

6

Thank you sir.