[gmx-users] Determining the energy of an individual atom.

[Darrell Koskinen]

Dear GROMACS Gurus,
In my simulation of a graphene structure surrounded by an ammonia gas, I 
am not seeing any adsorption of the ammonia molecules onto the surface 
of the graphene structure. I am wondering if the reason I am not seeing 
any absorption is because the graphene lattice is vibrating and thereby 
imparting too much energy to the ammonia molecule when it comes into the 
vicinity of the graphene lattice, thus impairing any adsorption. I 
assume that the adsorption energy would have to be significantly greater 
than the vibrational energy in order to allow adsorption to occur. If 
this is true, then is there some way of determining the translational 
(vibrational) energy of an atom in the graphene lattice so that I may 
compare it to the adsorption energy?

Thanks again for your help.

Darrell