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? 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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