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

[Nima Soltani]

Excuse me for the previous massage. It was corrected here:
> 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 my ​​manuscript is Force-Field ​papers.
(Golp-CHARMM and AgP-Charmm FFs) I can not understand about the
relationship of this figure to ​the Force-​​field? 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
>
>
> Best Regards,
> Nima Soltani
> ----------------------------------------------------------
> MSc. of Physical Chemistry
> Sharif University of Technology.
> =================================
>
> On Mon, Nov 7, 2016 at 7:47 PM, Nima Soltani <nima.slt at gmail.com> wrote:
>>
>> 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 my ​​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
>>
>