[gmx-users] Ions close to protein

David Mobley dmobley at gmail.com
Tue May 23 19:20:52 CEST 2006


> >When I add ions to my system to neutralise it some are placed quite close to the protein (even when using random) and in other cases during simualtions I have seen ions move into the protein, is this normal/okay and are there any ways of keeping these ions away from the protein?

In terms of keeping them away from the protein, not too sure. But I
think it is right to be nervous about ions that move into your
protein. These could have long correlation times.  Depending on how
long the correlation times are, you might need to run longer to get
adequate sampling. On the other hand, if your salt concentration is
reasonable, you might have enough ions that this behavior will
appropriately average out, especially if correlation times are
relatively short.

Probably, the overall answer to whether this is okay depends on what
question you are trying to ask. My personal opinion is that ions are a
whole can of worms that is mostly unopened so far, but sooner or later
someone will have to open it and it will be messy (long correlation
times, bad parameters, and strongly influence certain things). But
perhaps I'm just being pessimistic. And, in fairness, I should say
that so far I've decided just to ignore the issue, because I don't
want to be the guy who opens the can of worms.


> >
> >
> This is normal in the sense that it certainly happens in the real systems.
> The fact is that you probably don't want the ions to go mess up with your
> protein !!
> One solution:
> 1)order your solent in function of the distance to the protein, trjorder
> does this.
> 2)generate an index where you separate your solvent into the close and far
> from the protein.
> 3) then use genion giving this index and choose the index far from protein.
> Note that this won't ovoid the contact ion-protein during your simulation !!
> XAvier
> --
> ----------------------------------
>  Xavier Periole - Ph.D.
>  Dept. of Biophysical Chemistry / MD Group
>  Univ. of Groningen
>  Nijenborgh 4
>  9747 AG Groningen
>  The Netherlands
>  Tel: +31-503634329
>  Fax: +31-503634398
>  email: x.periole at rug.nl
>  web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
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