From: Alec Zander (
Date: Mon May 13 2019 - 12:12:42 CDT

Hello -
Depends on what type of micellar molecules you have, but generally there is
a head group and a tail group. If the micelles are stable on your
simulation timescale, head groups should always be positioned to be lining
the interior, so you could develop distance based selection criteria for
counting waters that are touching head groups, (first internal layer) and
then the waters that are touching those (second internal layer), and so
forth until you've counted all the waters on the inside. I suppose it will
be sensitive to tail length, lipid dynamics, and water infiltration though.

On Mon, May 13, 2019 at 12:56 PM Nick Palmer <> wrote:

> Hello everyone,
> I am simulating two reverse micelles and I need to be able to count the
> number of water molecules that are in each reverse micelle and out in the
> solvent for each frame of the simulation. What would be the best way to
> determine whether or not a water is inside one of these reverse micelles or
> not? I had tried to find all the waters within a certain amount of distance
> of the center of mass, but this only works when the two reverse micelles
> are not next to each other. Also, they don't stay the same shape the whole
> time so I would have to change the distances at every frame. Is there a way
> I could use the SASA of the reverse micelle to define a layer, so that I
> could count the number of water molecules inside and outside of each
> reverse micelle?
> Another issue I have been having is that sometimes the reverse micelles
> move across periodic boundary conditions, which seems to shift the center
> of mass for the micelles. How could I use pbc tools to solve this problem
> since these molecules are not directly attached to each other?
> Thank you very much in advance!
> --
> Nicholas J. Palmer