From: Giacomo Fiorin (
Date: Wed May 15 2019 - 08:47:13 CDT

If you have used "within" as space-based selection keyword, consider using
"pbwithin", which is the same thing but following the mininum-image


On Tue, May 14, 2019 at 11:05 PM Nick Palmer <> wrote:

> I have been able to use Alec's idea to get all the waters inside of the
> reverse micelle. Thank you both very much!
> Now my primary question is how to keep the reverse micelles in a single
> periodic image? How can I use PBC tools to keep groups of atoms that aren't
> attached to each other in the same image?
> On Mon, May 13, 2019 at 2:35 PM Vermaas, Joshua <>
> wrote:
>> One method where I've had some success determining "inside" and "outside"
>> are to use algorithms in computer vision applied to water densities. That
>> can define an "inside" and an "outside", which can be converted into a
>> volumetric density field that you can use to select atoms with (eg volume >
>> 0 for inside and <0 for outside). Its a fun problem, but not one where I'm
>> aware of a built-in solution.
>> -Josh
>> On 2019-05-13 12:15:19-06:00 wrote:
>> 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
> --
> Nicholas J. Palmer

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD