[gmx-users] question

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Tue Nov 22 20:11:48 CET 2016


I assume you meant some water molecules was located in the middle of
bilayer while adding solvent, right?

If yes:
Please have a look at this article for solvation part:

Kandt, Christian, Walter L. Ash, and D. Peter Tieleman. "Setting up and
running molecular dynamics simulations of membrane proteins." *Methods*
41.4 (2007): 475-488.

I am sure it helps.

You can also build your bilayer with Charmm-GUI and start from output


On Tue, Nov 22, 2016 at 12:01 PM, ÁLVARO RODRIGO RUIZ FERNÁNDEZ <
arruiz at ug.uchile.cl> wrote:

> Dear gromacs users:
> I need to build a phospholipid bilayer, but for some reason it gets water,
> I
> think the problem could be solved with the construction of a  plane that
> prevents the passage of water molecules. In short, can GROMACS generate a
> plane that prevents the passage of one type of molecules?.
> Thank you very much.
> --
> *Álvaro Rodrigo Ruiz Fernández Laboratorio Fisicoquimica
> MolecularDepartamento de QuímicaFacultad de CienciasUniversidad de
> Chile*Mobile:
> +56-9-75643659
> Office: +56-2-9787443
> arruiz at ug.uchile.cl
> --
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