[gmx-users] genion

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Dec 21 16:39:05 CET 2005


hi

On Wednesday 21 December 2005 16:26, Tamas Horvath wrote:
> I have a protein in water system. The protein has some charge, which I want
> to neutralise, introducing stochastic ammount of K+ or Cl-. As far as I
> figured out, the best way to do it is to use genion. Only I don't know
> beforehand what the protein's charge would be, so I'm wondering if it's
> possible to tell genion to neutralise the system?

look at grompp output, theres somewhere charge of the system.

> 
> 2nd.: If genion puts some ions in the system, are the ions considered as a
> 2nd protein?
> 

no you have to add them to your topol.top file manually and also if you use
t/p couple you have to add them to your mdp file.


> Hota
> 
> On 12/21/05, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> >
> > Hi Tamas,
> >
> > You have to specify it yourself.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 12/20/05, Tamas Horvath <hotafin at gmail.com> wrote:
> > >
> > > I want to neutralise my system (chargewise), so I use genion for that.
> > > Do I always have to specify the number of ions to use, or is there a way
> > > to automatically neutralise the system?
> > >
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> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> > Dept. of Biophysical Chemistry
> > University of Groningen
> > Nijenborgh 4
> > 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> >
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> 
greetings,

florian


-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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