[gmx-users] water in channel

Jocelyne Vreede vreede at science.uva.nl
Tue Jan 20 16:46:02 CET 2004

Dear Itamar and Anton, 

A while ago I had similar problems with genbox: the program wrongly
inserted water molecules in a protein. I solved it by clustering water
molecules on the basis of hydrogen bonds. If a water molecule forms a
hydrogen bond to a water molecule of the cluster, it is added to the
cluster, otherwise a new cluster is created. 
This way, the bulk solvent is represented as one single cluster, whereas
additional clusters identify water molecules that are isolated i.e.
inside the protein or lipid bilayer. 

If you are interested, I can send you the code (in C). 



> 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...
Jocelyne Vreede, M.Sc.
SILS - Microbiologie
Universiteit van Amsterdam
vreede at science.uva.nl

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