[gmx-users] genion

[Tamas Horvath]

Of course I can, but the only way to do that is to capture the pdb2gmx or
grompp output as it seems...

On 12/21/05, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
>
> hi,
>
> On Wednesday 21 December 2005 17:53, Tamas Horvath wrote:
> > The thing is, I'm working with literally thousands of proteins, and
> running
> > some basic simulations on them. Therefore I need to run these
> simulations
> > using scripts, so I guess u can't expect me to know every charge
> > distribution... These simulations may well be worthless and bogus, but I
> try
> > to do my best to make them meaningful...
>
> you can change your script  so it can automatically neutralise your
> systems.
>
>
>
> >
> > On 12/21/05, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > >
> > > 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?
> > >
> > > Not knowing the pattern of charge distribution in your protein, and
> thus
> > > the net charge, sounds to me like a great way to run the risk of doing
> > > some worthless simulations and/or bogus science for want of a few
> > > minutes of observation and thought. I'd call the gromacs utility
> > > programs' inability to automatically neutralise a system a feature,
> not
> > > a bug!
> > >
> > > Cheers,
> > >
> > > Mark Abraham
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> >
>
> Greetings,
>
> Florian
>
> --
>
> -------------------------------------------------------------------------------
> 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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