[gmx-users] Placing water molecules in a defined space in the model

[Agnivo Gosai]

Hello users,

I am trying to prepare a topology containing an alkanethiol layer and a
protein moelcule above it for a MD simulation using GROMACS 4.6.7.

For this, I want to place the water molecules in the layer in such a way
that they only occupy the space above the alkanethiol layer.

To accomplish this , do I need to create a simulation box such that the
layer lies on one face / side of the box (rectangular) and then use genbox
tool ?

Or there is some other method ? I have provided a link containing the
preliminary pdb file of my system. Kindly suggest.

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 molecule.png
<https://drive.google.com/file/d/0B-U8uULVZjfRaUhmNXB0RU9rZk0/view?usp=drive_web>
​
Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.