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
> Anything wrong???
> Any suggestion would be highly appreicated.
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.
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
More information about the gromacs.org_gmx-users