Ben,
Thanks for the reply. I am using POPC+cholesterol bilayer system. In
my case only a part of the protein (1-20 residues) goes into the lipid
bilayer. So, I have capped rest of the protein with solvent and
counter ions. I found few articles where the protein was completely
immersed into the bilayer. I am currently struggling to establish a
particular simulation procedure for my system. As you have mentioned
before, initially I have minimized the system for 10,000 steps by
constraining protein, lipid, and cholesterol molecules. Then, heated
the system (0-100K) for 10ps under NVT conditions (with protein
constrained) and then (100-300K) under NPT conditions (with protein
constrained). Then, under NPT conditions the system was equilibrated
without any constraints.
But after 1-2 ns of simulations, I have observed a large void in the
protein. Is there any alternative procedures? Please let me know
about it.
mani
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Received on Tue Jan 15 2013 - 10:00:02 PST
