[gmx-users] genion

Björn Windshügel bjoern.windshuegel at pharmazie.uni-halle.de
Tue Mar 1 08:36:03 CET 2005

> Dear All,
> I used "genion" to add a Cl- to neutarlize my system. But I just noticed
> that the Cl- was put within the protein. Is it supposely like this???
> My understanding is that Cl- should  be in the water box but far away from
> the protein to make sure not to interfere the interactions from the protein
> itself.
> Anything wrong???
> Any suggestion would be highly appreicated.
> nancy

Just use the -random option and try different seeds. Genion sometimes places 
ions at unfavourable sites. By trying different values for the seed you will 
finally get a chloride outside the protein.


Björn Windshügel
Institut für Pharmazeutische Chemie		
Martin-Luther-Universität Halle		email:	windshuegel at pharmazie.uni-halle.de
Wolfgang-Langenbeck-Str. 4		phone:	(49)345 55-25043
06120 Halle (Saale)				fax:		(49)345 55-27355

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