Hello,
I'm having a small but significant problem with simulating a protein
inserted in a DPPC membrane. I have simulated the system for 15 ns with
position restraints on the protein to allow the lipids to anneal around it,
but have recently found a small problem. I found a small gap between the
protein and lipid where some water molecules embedded themselves. Is there
any way I can change the parameters of the simulation to remove these
waters, so that the lipids will aggregate properly around the protein? What
would the best solution be? Should I just remove these waters manually?
Thanks,
Max Macaluso
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