VMD-L Mailing List

From: Nick Palmer (tuf90798_at_temple.edu)
Date: Mon May 13 2019 - 11:26:22 CDT

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