[gmx-users] genion

[Tamas Horvath]

So, the bottomline is, that I have to capture e.g. the grompp output to
determine the net charge?

On 12/21/05, Tamas Horvath <hotafin at gmail.com> wrote:
>
> 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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