[gmx-users] amino acid on solid surface

[Alexander Alexander]

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