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So far i have found only one paper that describes how we can compute protein energy while doing MD simulation:

Can you propose more papers for protein energy computation?

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    $\begingroup$ I don't get the issue here. For each step in MD, you can get the system energy calculated with the used force field. Nothing new here. BUT, if you want to calculate the binding free energy between the ligand and the protein, it is also possible but in general using a third party software. $\endgroup$
    – Camps
    Oct 6, 2023 at 20:02
  • $\begingroup$ @Camps, I didn't get your comment. can you rephrase it? $\endgroup$
    – user366312
    Oct 6, 2023 at 20:05
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    $\begingroup$ It's not clear what you mean by "protein energy". Do you mean the total potential energy of all internal protein interactions? The total energy (including solvent interactions and kinetic energy)? Binding energy between a protein and ligand? Or some free energy, which includes pressure and entropy terms? $\endgroup$
    – Hayden S
    Oct 6, 2023 at 22:20
  • $\begingroup$ @HaydenS if it's the mass-equivalence energy, that's particularly straightforward. You just multiply by the speed of light squared and you get 2e10 kcal/mol/Dalton. :) $\endgroup$ Oct 6, 2023 at 22:26

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