[gmx-users] about potential energy calculation

[Mark Abraham]

Hi,

Having low potential energy (whether in dynamical simulation or em) and
being (any kind of) stable are nearly unrelated concepts. There may be a
way to measure what you want, but so far I suspect you haven't worked out a
good way to describe what you want.

Further, unless your peptides are isomers, your potential energies are of
systems with different composition, so can't be compared.

Mark

On Fri, 13 Jan 2017 09:31 Albert <mailmd2011 at 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 reliable?
>
> Thanks a lot
>
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