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How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?

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    $\begingroup$ Please corrects tags, as gromacs cannot do quantum dynamics. $\endgroup$
    – Anon
    Commented Oct 24, 2023 at 20:50
  • $\begingroup$ Are you talking about the adsorption of a single napthalene molecule on the sheet of GO? What are you planning to compute by MD with this? If you run the simulation for long, you keep a single napthalene molecule inside a box of GO sheet, it will adsorb the napthalene. $\endgroup$
    – Roshan Shrestha
    Commented Oct 25, 2023 at 7:37

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There are a couple of strategies that I know of in the literature. The first one is the so-called chemical vapour deposition. It is fairly easy to script, you can find details on the procedure in this paper.

The other strategy I have read consists of implementing a solvent evaporation scheme. Details to be found in this paper.

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  • $\begingroup$ i'm new user of gromacs and i dont have any ideas how to prepare the input files? all existing tutorials it for proteins-ligand $\endgroup$
    – Mohamed El-amine
    Commented Oct 25, 2023 at 8:26
  • $\begingroup$ Essentially you need parameter files and coordinates for each molecule in your system. You can search for these in the literature or online (see github.com/arvpinto/GO_sheets for example), and once you find them write again for further indications on how to set up the stuff. You will need to verify that the two sets of parameters can be used together and that they give reasonable results for properties you are interested in. $\endgroup$
    – Anon
    Commented Oct 25, 2023 at 17:53
  • $\begingroup$ thank you for all explanations $\endgroup$
    – Mohamed El-amine
    Commented Oct 26, 2023 at 8:49
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The set-up for the MD simulation depends on what you want to observe or what quantities you want to compute. If you want to set-up the MD simulation of the adsorption of a single Naphthalene molecule on graphene-oxide (GO), then it is straightforward. Just have the AA parameters for both molecules and in a box with the GO sheet, insert a molecule of Naphthalene in it. You will see that if you run the simulation for long, the molecule will adsorb onto the surface of GO. So, all you need is the AA parameters for both GO and Napthalene. For that, do some literature search, and see if the GO has been parametrized well enough, and if there are some previous works done with this regard.

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    $\begingroup$ I gave my +1 yesterday but congrats on reaching 1000! $\endgroup$
    – Nike Dattani - No Free Time
    Commented Oct 26, 2023 at 5:31
  • $\begingroup$ Thanks @NikeDattani. I will try to contribute more in the future if the topic is relevant to my research :-) $\endgroup$
    – Roshan Shrestha
    Commented Oct 26, 2023 at 6:45
  • $\begingroup$ thank you for all explanations :) $\endgroup$
    – Mohamed El-amine
    Commented Oct 26, 2023 at 8:48

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