[AMBER] potential energy

From: Albert <mailmd2011.gmail.com>
Date: Fri, 13 Jan 2017 09:42:08 +0100


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 more reliable?

Thanks a lot

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Received on Fri Jan 13 2017 - 01:00:02 PST
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