[gmx-users] water in channel

[Eric Jakobsson]

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.)