From: Norman Geist (
Date: Tue May 14 2019 - 01:17:08 CDT



a colleague of mine once wrote a TCL wrapper for the Voro++ lib to measure molecular volumes inside VMD. I’m pretty sure this would also serve to determine if waters are within that volume of the micelles. If you are interested I can give you the contact.



Norman Geist


Von: [] Im Auftrag von Nick Palmer
Gesendet: Montag, 13. Mai 2019 18:26
An: VMD Mailing List <>
Betreff: vmd-l: Defining a layer for a micelle


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