[gmx-users] water in channel

David L. Bostick dbostick at physics.unc.edu
Mon Jan 19 17:33:01 CET 2004

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 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.
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