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! :-)
Mark
Thanks again for your help.
Darrell
Date: Wed, 12 Aug 2009 13:42:08 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Determining the energy of an individual atom.
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a823a10.6010...@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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