[gmx-users] water in lipid bilayer

[Mark Abraham]

N-J.M. Macaluso wrote:
> Hi,
> 
> I'm performing a transmembrane protein simulation in an explicit DPPC 
> bilayer. I manually removed the lipids to accomodate my protein and the 
> system has undergone 15 ns of equilibration.
> 
> In removing the lipids, I a gap betwteen the protein and membrane 
> resulted. Most of the lipid molecules aggregated around the protein, but 
> I have found that on one side of the protein, there are some water 
> molecules that have found their way between the protein and lipid 
> bilayer. Is there any way of removing these by altering the simulation 
> parameters, or will I have to remove them manually? 

See http://wiki.gromacs.org/index.php/Membrane_Simulations... these 
waters may have been present in your initial structure.

> I already 
> constrained the waters in the z-direction at the start of the 
> simulation, so that didn't work in this case.

I don't understand this.

Mark