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
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