[gmx-users] genion

[Florian Haberl]

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

-- 
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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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