Dear Zeynab,

I think you could estimate the adsorption energy by picking the absorb and desorb structures and minimizing them. If those structures are stable enough you could obtain each energy state by minimizing them. I don't know how complex your system is, but I guess this could help.

Veronica

Dear Zeynab,

Probably, you could use a QM/MM simulation, but be careful when applying the interaction between your acid and CNT surface. As Veronica Sanchez mentioned, it would depends on how complex your system.

Best,

Viny

Hi Wojciech,

Thanks for the answer. Which amino acid distance from the CNT surface is considered as the desorption state? Maybe stupid but I wonder if the whole process of desorption-readsorption is considered as a kind of adsorption state or not.. That is becouse otherwise why when it seprates it adsorb again.. Do you have any idea about it?

Moreover I have another question: Does in my case the umbrella sampling method is applicable? If so, does this method give me an exact value of the binding energy?

Salam sister Zeynab,

If you try to calculate the adsorption of alpha amino acid inside a single or multi_walled carbon nanoute of radius less than 5 Angstrom, this leads to rejecting the certain amino acid because of forming air plug. I think there is a possibly to calculate the interaction energy numerically by performing the surface integral for each interacting molecule, but the minimum of interaction energy would be very small. The best method is to use the discrete approach by splitting the amino acid into two or three sub_configurations