[gmx-users] water in lipid bilayer

N-J.M. Macaluso njmm2 at cam.ac.uk
Mon Nov 19 11:30:56 CET 2007


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

Thanks for your time, I would appreciate any advice.

Max Macaluso

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