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Context:

If I have a system that consists of 20 structures. During molecular dynamics, these structures can form micelles from my point of view.

I would like to do the following:

  1. Confirm if the micelle is stable
  2. Confirm that the micelle can be formed and that there is no water inside (i.e., there is no water close to the hydrophobic part and there is water close to the hydrophilic part).

To do point 2, I used VMD to calculate the radial distribution function, and I selected one atom of the structure and one atom of the water solvent. But the g(r), as you see in the figure, is very small, and I don't know why. I am thinking that maybe because I selected one atom of the structure that already has the same name as the other 19 structures, therefore the calculated g(r) is an average for the 20 structures.

Question(s):

  1. How can I confirm the stability of the micelle?
  2. How can I confirm that the micelle can be formed and that there is no water inside?
  3. Why is the g(r) so low?

Radial Distribution:

Radial_distribution

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  • $\begingroup$ If you are trying to understand the stability of water networks, have a look at this link However if you are trying to understand if there are any water molecules within the micelle, you might want to define a function that takes a value of 0 or 1 depending on if water is present in the micelle. $\endgroup$ May 3, 2023 at 13:49
  • $\begingroup$ @Mohamed Please make a note of the edits I made. It now makes it much easier for people to answer your question(s). Previously it was a bit fuzzy. Hope Camps answer helps you :) $\endgroup$ May 4, 2023 at 12:09
  • $\begingroup$ @VandanRevanur Thank you. Yes, now it is nice $\endgroup$ May 4, 2023 at 12:50

1 Answer 1

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Here are my two cents (things that I would try):

  1. How can I confirm the stability of the micelle?
    You could run the simulation for a longer time and/or run at different temperatures. Also, monitoring the energy during the simulation time.

  2. How can I confirm that the micelle can be formed and that there is no water inside?
    It is possible to do a topological study and search for bond critical points. Also, if you start from different initial distribution and at the end, you have a conglomerate of your structures, then the micelle is formed. About the water inside, the g(r) is a good measure. I recommend the software TRAVIS. It has several functions to study the distribution of particles from molecular dynamics trajectories.

  3. Why is the g(r) so low?
    One possible cause can be the atom selection, as you already guessed. The TRAVIS software will identify all the molecules in your system and will calculate the g(r) from a reference molecule (or atoms that you choose) to an atom, molecule, or a set of atoms/molecules.

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