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

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 12 07:45:11 CEST 2009

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 van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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