[gmx-users] genion

[Tamas Horvath]

Thanks Alan, so the mysterious 2nd protein is indeed the new ions :)

On 12/21/05, Alan Dodd <anoddlad at yahoo.com> wrote:
>
> Discovering the protein's charge is pretty trivial -
> many programs in gromacs will give an error message
> for systems with a net charge, eg. pdb2gmx and of
> course grompp.  As you've got to run grompp for genion
> anyways, just do that and pay attention to the output.
> Ions are given a seperate group in the topology and
> .mdp files, as if they were a separate protein.
> You'll have to fix these parts yourself.
>
> --- Tamas Horvath <hotafin at gmail.com> 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?
> >
> > 2nd.: If genion puts some ions in the system, are
> > the ions considered as a
> > 2nd protein?
> >
> > 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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