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

[Mark Abraham]

Darrell Koskinen wrote:
> 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?

You can measure the average kinetic energy of an atom, but whether you 
can infer anything else might depend on comparing with a structure to 
which something did adsorb.

Frankly, it seems rather more likely that the ad hoc combination of 
parameters you have described in the past is incapable of modelling this 
behaviour. Parameterization is only known to be useful within a limited 
domain. You might be able to demonstrate transferability, but it cannot 
be assumed.

Mark