[gmx-users] Energy analysis

[Mark Abraham]

Hi,

Depends what you mean by "stability." A well designed study could seek to
measure or estimate the difference in the free-energy of folding, but that
would probably require an infeasibly large amount of sampling, and be
highly dependent on the quality of the parameterization of the
metal-protein interactions, for which you would probably need some suitable
experimental data.

Mark

On Sun, Nov 19, 2017 at 7:48 AM Amir Zeb <zebamir85 at gmail.com> wrote:

> Hi gromacs users,
>
> I want to calculate the energy for comparative analysis of protein with and
> without metal ion, wherein I would like to determine the influence of metal
> on protein structural stability. I have used gromacs for simulation. Please
> suggest me how to do this kind of analysis? Should i follow a specific
> tutorial?
>
> Amir
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