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 < alexanderwie...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
