[gmx-users] water in channel

[Anton Feenstra]

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...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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