I submitted MD simulation for two small peptides with Amber FF. I calculated the average potential energy of the system:

peptide A: -9x10^4 kcal/mol

peptide B: -6X10^4 kcal/mol

it seems that peptide A is more stable than B.

However, if I extract each frame the peptide from MD simulation and submitted to energy minimization, the results is different:

peptide A: -180 kcal/mol

peptide B: -230 kcal/mol

In this case, peptide B is more stable than A.

I am just wondering why the calculations of the two cases are different? Which one is reliable?

Thanks a lot

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