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?
If your graphene is not polarizable then the interaction with ammonia is
limited to Van der waals interactions. However the induced polarization
can be quite strong for such groups, and hence it seems you are missing
an important part of the binding energy.
Thanks again for your help.
Darrell
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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