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how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation enter image description here

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  • $\begingroup$ I look at that graph and I note the high ∆G at 0 Ångström and wonder if the reference pose for the RMSD was not energy minimised correctly... so maybe not the best reference. prody.csb.pitt.edu is a helpful toolkit for this kind of analysis. Is Python an option and what is your reference? (If any user knowledgeable about peptides sees this please step in as I doubt I can help —NMR works by magic, right?) $\endgroup$ Feb 18 at 12:00
  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Feb 18 at 14:06
  • $\begingroup$ Thanks for the comment .. i'm trying to use the tool but couldn't .. in which part please i can plot RMSD with energy surface ? $\endgroup$
    – sam
    Feb 18 at 19:42

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