[gmx-users] how to remove water molecule inside micelle?

André Farias de Moura moura at ufscar.br
Mon Dec 29 13:13:39 CET 2014

it's hard to say without knowing how you prepared and relaxed your micelle
before adding water, so I can only provide you a few general comments:

(1) a properly relaxed, well-packed micelle should not present any voids
and water should not go inside the micelle (check the literature, this has
already been done a number of times already for SDS and other surfactants)

(2) increasing the value for -vdwd should decrease the number of water
molecules inside the micelle, even if the preparation step was not
accomplished so carefully.

(3) maybe you could try Packmol:

On Mon, Dec 29, 2014 at 5:39 AM, Mina Hashemi <hashemi.mina5 at gmail.com>

> Dear gromacs users
> I prepared my simulation system containing SDS.
> Then I added water molecules using genbox. Some water molecules
> entered in to the micelle.
> How to remove water molecules inside the micelle?
> Any help will highly appreciated.
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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