[gmx-users] genion

Tamas Horvath hotafin at gmail.com
Wed Dec 21 17:53:50 CET 2005

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...

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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