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:
- Confirm if the micelle is stable
- 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.
- How can I confirm the stability of the micelle?
- How can I confirm that the micelle can be formed and that there is no water inside?
- Why is the g(r) so low?