[gmx-users] about potential energy calculation

Albert mailmd2011 at gmail.com
Fri Jan 13 09:30:55 CET 2017


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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