[gmx-users] How to describe the Dynamic equilibrium between two states?

[Nima Soltani]

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​