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

Nima Soltani nima.slt at gmail.com
Mon Nov 7 10:34:08 CET 2016

Hello dear GROMACS users
I have recently submitted a manuscript
​ ​
​ ​
​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
should be discussed.
​" "​

Fig 3 is radius of gyration as a function of time and it's link is provided


 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 ​

 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
​ ​

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