Hello dear GROMACS users I have recently submitted a manuscript about studying interactions of peptide-surface system.
one of the referees has asked that : " "For the adsorption of the peptide on Au(111) in Figure 3 it seems that there is a dynamic equilibrium between two states (with Rg=0.8 and Rg=0.9). The difference is noted in the text (pg 9), but no attempt is made to explain this behavior. Is there a link to binding energies ? How does this fact compare with the cited work of Ref 54/55 ? Also the different adsorption kinetics (timescale needed for adsorption) for different surface s should be discussed. " " Fig 3 is radius of gyration as a function of time and it's link is provided here: https://app.box.com/s/jpa4n5z796aht80d78tvrd7qpiyns31z Refrence 54 and 55 of m y manuscript is Force-Field papers. (Golp-CHARMM and AgP-Charmm FFs) I can not understand about the relationship of this figure to the Force- F ield? What measure or analysis is considered appropriate to explain this "Dynamic Equilibrium" and cite this question ? Is it possible to study adsorption kinetics from one simulation? Millions of thanks in advance for any tips or guidance Nima -- 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.
