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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 13 03:23:56 CEST 2009

Darrell Koskinen wrote:
> 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?

Well you'll need to have recorded velocities (nstvout) and use one or 
other of the utility programs to analyze your .trr. See manual 7.4 to 
see what might be useful, and then relevant sections of Appendix D.

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

That's a good start! :-)


> Thanks again for your help.
> Darrell
>> 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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