Are the peptides chemically identical? If not, this comparison is not
valid.
On Jan 13, 2017 3:42 AM, "Albert" <mailmd2011.gmail.com> wrote:
> Hello:
>
> 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 - 03:30:02 PST
