Dear LAMMPS users and developers,
I want to covalently bind a functional group such as COOH on the surface of a nanoparticle. The constraint is that the percentage of surface coverage by these functional groups should be such that the thermodynamic laws be satisfied.
I couldn’t find in the literature what is the equilibrium surface coverage of my nanoparticle of interest by the aforementioned functional group. Although I could write a code to cover the surface of nanoparticle by functional group, I think this method cannot result in an equilibrium surface functionalized structure.
I did a research though LAMMPS documents and mailing list and the only existing function I found in LAMMPS that might help me is “fix gcmc”. But, it seems this fix works well with a reservoir of small sized gases, not the functional groups I want to work with.
Can anyone please provide some guidance with me regarding if LAMMPS can provide any way of handling this issue.
The best,
Farshad
Fix GCMC can't do what you're looking for here since it involves making and breaking covalent bonds. Furthermore, I doubt there's existing functionality in LAMMPS that could build your structure as you describe. You're probably better off writing your own code to do it, but as you note, it might be difficult to rigorously meet your constraints. If you only cared about achieving some known percent coverage, that would certainly simplify your task.
Paul
Dear LAMMPS users and developers,
I want to covalently bind a functional group such as COOH on the surface of a nanoparticle. The constraint is that the percentage of surface coverage by these functional groups should be such that the thermodynamic laws be satisfied.
what thermodynamic laws? according to what measurements? how is the
kind of nanoparticle you're looking at characterized anyway? and what
is the typical size? does it even fit into a typical size MD
simulation?
I couldn’t find in the literature what is the equilibrium surface coverage of my nanoparticle of interest by the aforementioned functional group. Although I could write a code to cover the surface of nanoparticle by functional group, I think this method cannot result in an equilibrium surface functionalized structure.
so you will first need to study: a) how much it matters, and b) what
the various free energies for the possible attachment processes are.
b) is probably enough work for an entire PhD thesis alone, as i would
imagine it may require complex collective variable calculations for a
number of possible reactions pathways to map out a suitable free
energy hypersurface.
I did a research though LAMMPS documents and mailing list and the only existing function I found in LAMMPS that might help me is “fix gcmc”. But, it seems this fix works well with a reservoir of small sized gases, not the functional groups I want to work with.
Can anyone please provide some guidance with me regarding if LAMMPS can provide any way of handling this issue.
even if there was some functionality in LAMMPS to do this, you will
*still* need to parameterize it, i.e. know various probabilities or
energies. where should these come from?
it is not so much a question of LAMMPS being able to handle the
simulations, but it is a matter of *planning* a set of simulations.
and there is no MD code that can do this for you.
axel.
Dear Axel,
Thanks for providing your detailed answer to my question. As a matter of fact, my particle is a 5 nanometer size carbon nanoparticle which has large surface area.
When I was asking my question, I didn’t want to go too much into the details to not get my reader tired of reading my question, though I knew I am taking the risk of raising some fundamental questions about problem.
As you explained, it’s a very complicated task which I am still investigating about how to do it. It seems to me that I have to write my own code to handle this problem.
The best,
Farshad
Dear Paul,
Thanks for clarifying this point for me that Fix GCMC is designed to do the tasks other than what I want to use.
The best,
Farshad
Dear Axel,
Thanks for providing your detailed answer to my question. As a matter of fact, my particle is a 5 nanometer size carbon nanoparticle which has large surface area.
When I was asking my question, I didn’t want to go too much into the details to not get my reader tired of reading my question, though I knew I am taking the risk of raising some fundamental questions about problem.
that is nonsense. you cannot get good help on vague and incomplete
information. ...and there is nothing more irritating than having to
ask a ton of questions to get the necessary details or having to guess
and risk giving bad advice. also, by describing your problem in such a
vague fashion you make yourself look less knowledgeable and competent.
on the other hand, a person that can provide helpful advice will
always appreciate specific and detailed information (not "everything",
but everything *relevant*). everybody doesn't matter, so they may get
tired of it. you don't lose anything. think about it.
p.s.: what is *even more* irritating is to have been forced to ask
questions and then not get them properly answered.