From: dhacademic (dhacademic_at_gmail.com)
Date: Sat Jul 03 2010 - 10:20:23 CDT
I have one question about membrane-protein simulations with NAMD.
In my system, it is a channel structure merged into the membrane. In its
closed state, the topology looks like “/\”, and the bottom part of the
channel is wide enough (the radius of the pore is ~8 angstrom) to
accommodate some water, even though the top part is closed. In the open
state, it looks like ‘| |’, and more water can get into the pore.
I know the dehydration of membrane-protein interface is important in the
simulations. According to the “membrane protein tutorial”, a “keep water
out.tcl” can be used to pump out water from the hydrophobic region. During
the equilibrium and production states, this region should be inaccessible
for water. However, I am not certain about the hydration in channel. In my
opinion, the hydration inside the channel region (which has enough space to
accommodate water) is reasonable, and there is no reason for a wide channel
to be vacuum. I want to know if it is necessary to do the following
restraint before production stage: making the interior of channel within the
membrane to be dehydrated as the initial structure, and keeping this
dehydration along the equilibration.
Can anyone give some comments on this issue? Many thanks.
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