Re: hydration in membrane-protein simulations

From: Chris Harrison (
Date: Tue Jul 06 2010 - 09:36:22 CDT

Since dehydration of the protein surface is likely a gradual process
occurring concurrently during transition between conformational states of
the protein, it is not clear what you are attempting to accomplish by
dehydrating the beginning "/\" state.


On Sat, Jul 3, 2010 at 10:20 AM, dhacademic <> wrote:

> 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.

Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078

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