From: zeynab mohamad hoseyni (zmhoseyni_at_yahoo.com)
Date: Mon Feb 03 2014 - 10:27:20 CST
I'm pretty new in the membrane simulation. I followed the NAMD tutorial to put my Trans-Membrane (TM) protein
in the lipid bi-layer. I then followed the preparation steps containing 1)melting the lipid tails, 2)minimization of the whole
system, 3)NPT equilibration with constrained protein (where we use keep_water_out.tcl too) and 4)NPT with released protein
(without using keep_water_out.tcl). I then did 11ns of NPT simulation.
I observe that at the step 4 when we release the protein and turning off the keep_water_out.tcl script, some water molecules
start to penetrate in a small cavity on the TM domain (TMD) of the protein close to the protein water interface. One of them
tries to cross the lipid bi-layer and go to the other side of the membrane through passing via lipid tails which may face the
the hydrophobic repulsive force of lipid tails and coming back to the TMD of protein in where it traps in the middle.
Other water molecules in the cavity stay there during the rest of the simulation up to 11ns. One more water penetrates the
lipid bi-layer at the edge of periodic cell which I guess might be expected as the I left 1A extra of cell vectors for the lipid expansion.
I'm not sure if the mentioned observations are true. Can you guide me if you have any experience with that?
All the Best,
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