Hi I did umbrella sampling and calculate PMF for different aminoacid in different distance from surface. Now i want to discuss about the results. First i used gmx sasa to prove that for example amino acid(tyrosine) with more surface (it's aromatic) had more binding energy in comparison to another... But sometimes its hard to compare different AA, so i want to calculate AA's polarizability. Is there any analysis in gromacs to calculate that? If yes, is it probable that i get wrong results because some aminoacids are not too different in size and polarizability? And are in SOL, so may affect all these properties? Do you have better idea?
Thank you so much Rose -- 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.