[gmx-users] amino acid on solid surface

[Mark Abraham]

Hi,

Why aren't you looking at distance between surface and adsorbant as a
criterion?

Mark

On Wed, Jun 22, 2016 at 11:24 AM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> Dear Gromacs user,
>
> I am simulating the adsorption behavior of single amino acid or a short
> peptide into a solid surface in water, after all the minimisation,
> equlibrsation, and production,  how should I find out if the amino acid has
> been absorbed?
>
> Does RMSD help? I calculated the RMSD for amino acid, its backbone and
> mainchain, respected to their minimized situations. Their RMSD crazily
> oscillate first for a while and then somewhere after 15 or 20 ns, they just
> ranging between 0.05 and 0.12. Do you think this means adsorption?
>
> Thanks.
> Best regards,
> Alex
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