[gmx-users] water in channel

Rainer Boeckmann rainer at bioc.unizh.ch
Tue Jan 20 10:07:01 CET 2004

one way to avoid water being placed inside the bilayer is to increase 
the radii in vdwradii.dat.

Anton Feenstra wrote:

> 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? 
> From what I hear, water inside bilayers occur often when using genbox.
> Some people argue about whether it is a problem, but usually the only
> way to solve it is to remove them 'manually'. That is probably easier
> than it sounds, based on the Z coordinate you can easily identify them,
> but then you include some at the center of the protein. THese you can
> identify by now looking at the location in the x-y plane, or you could
> look at their distance to the protein. Probably, some of the membrane-
> guru's have scripts that may make this easier...

Dr. Rainer Böckmann
Computational Structural Biology - Biochemistry Department
University of Zürich
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
tel:    ++41-(0)1-63-555-93 - fax:    ++41-(0)1-63-568-62
email: rainer at bioc.unizh.ch

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