[gmx-users] water in channel
feenstra at chem.vu.nl
Tue Jan 20 10:01:01 CET 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?
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...
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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