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

Darrell Koskinen darrellk at ece.ubc.ca
Thu Aug 13 01:02:11 CEST 2009

Hi Mark,
I do have a paper in my possession that provides a first principles 
calculation of the adsorption energy of ammonia on graphene. I was 
planning on using this paper to compare the adsorption energy to the 
vibrational energy of the individual atoms in the graphene lattice. But 
how do I measure the average kinetic energy of a graphene atom in my system?

And I should also let you know that I have removed the ad hoc parameters 
and am using ffoplsaa in its pure unmodified form.

Thanks again for your help.

> Date: Wed, 12 Aug 2009 13:42:08 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Determining the energy of an individual atom.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A823A10.6010903 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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

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