[gmx-users] water in lipid bilayer
Mark.Abraham at anu.edu.au
Mon Nov 19 12:14:03 CET 2007
N-J.M. Macaluso wrote:
> 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.
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