[gmx-users] Ions close to protein

Xavier Periole x.periole at rug.nl
Tue May 23 17:09:56 CEST 2006

Joanne Hanna wrote:

>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?
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 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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