[gmx-users] water in channel

[David L. Bostick]

Yes, Eric is right..

Generally speaking, something like Dowser will work in more cases.
However, it should usually be easy to judge whether approach #2 will work.
For example, gramicidin is well known to have conduction bursts for all of
its permeant species that are spaced apart on a timescale that is too long
to simulate using MD. These bursts have been attributed to blockage by
lipid headgroups neighboring the gA channel.  Indeed, from experience, once
a headgroup has bound to the mouth of the gA pore, it will never saturate
with water from the aqueous bath.  The important observation is that the
length of the gA channel is quite a bit shorter than the average width of
the bilayer.  So, I would say that approach 2 will probably work when the
channel length is sufficiently greater than the bilayer width.  Many
channels should satisfy this criterion. Of course you will need to position
restrain all atoms in the channel while the channel saturates to full
occupancy to avoid any deformation problems.

But if you want to be sure to get it right the first time, try approach #1.

David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Mon, 19 Jan 2004, Eric Jakobsson wrote:

> Approach # 2) will not work for all channels.  We published a paper in
> Biophys. J. a number of years ago in  which we looked at water motion in
> the gramicidin channel with the protein immobile but the water at 300
> K.  The water moved locally in the normal way, but had no motion along the
> channel at all.   I am sure if we had started with the channel empty and
> the gramicidin frozen, it would never have filled, at least not in any
> reasonable time.  On the other hand, for some channels if you don't
> immobilize them and you don't have contents in the lumen, the lumenal
> structure will become unstable.  So approach # 1) (Dowser or some
> equivalent method) is the better way, based on our group's experience.
>
> Eric
>
> At 11:31 AM 1/19/2004 -0500, you wrote:
>
> >I can think of 2 options:
> >
> >1) There is a program called "Dowser" put out by J. Hermans' lab at
> >UNC-Chapel hill.  It usually works very well.
> >
> >2) You can position restrain the channel and allow water and bilayer to
> >move freely during MD.  It should not take long for water to enter the
> >channel ... that is, providing that it is actually supposed to do so. Water
> >is probably the fastest diffusing species in your system.  You can take
> >advantage of this.
> >
> >David
> >
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >David Bostick                                   Office: 262 Venable Hall
> >Dept. of Physics and Astronomy                  Phone:  (919)962-0165
> >Program in Molecular and Cellular Biophysics
> >UNC-Chapel Hill
> >CB #3255 Phillips Hall                          dbostick at physics.unc.edu
> >Chapel Hill, NC 27599                           http://www.unc.edu/~dbostick
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >
> >On Mon, 19 Jan 2004, Itamar Kass wrote:
> >
> > >   Hi all, I am currently working on a channel in a DMPC bilayer (and
> > water).  After inserting the channel into the bilayer (using  Graham's
> > modified mdrun) I am facing a new problem.   I want to put water in the
> > channel and did not succeed in doing it.  Using pr simulation I did not
> > succeed, then I tried to use genbox, but it puts water in the membrane also.
> > >   Does someone have an idea or face it and has a solution?
> > >           Thank you, Itamar.
> > >
> > > ********************************************
> > > Computers are like airconditioners... They don't work well with Windows
> > open.
> > > ********************************************
> > >
> > > ===========================================
> > > | Itamar Kass
> > > | The Alexander Silberman
> > > | Institute of Life Sciences
> > > | Department of Biological Chemistry
> > > | The Hebrew University, Givat-Ram
> > > | Jerusalem, 91904, Israel
> > > | Tel: +972-(0)2-6585146
> > > | Fax: +972-(0)2-6584329
> > > | Email: ikass at cc.huji.ac.il
> > > | Homepage:
> > http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> > > ============================================
> >
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> ---------------------------------
> Eric Jakobsson, Ph.D.
> Professor, Department of Molecular and Integrative Physiology, and of
> Biochemistry
> Senior Research Scientist, National Center for Supercomputing Applications
> Professor, Beckman Institute for Advanced Science and Technology
> 4021 Beckman Institute, mc251
> University of Illinois, Urbana, IL 61801
> ph. 217-244-2896       fax 217-244-2909
> (Currently on leave to the National Institutes of Health in Bethesda,
> Maryland, to be Director of the NIGMS Center for Bioinformatics and
> Computational Biology and Chair of the NIH Biomedical Information Science
> and Technology Initiative Consortium, but maintaining my research lab at
> Illinois by periodic commuting.  My usual schedule is four days a week at
> NIH and three days a week at Illinois.)
>
>
>
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