[gmx-users] counterions

Ran Friedman ran at hemi.tau.ac.il
Fri Oct 8 18:37:49 CEST 2004


People normally add counter ions to neutralise their system. It is also 
common to add a few salt ions in order to stabilise simulations of 
biomacromolecules (you can search pubmed for a publication by Ibragimova 
and Wade related to the subject) or simply to mimic physiological 

To the best of my knowledge, you should neutralise the total charge of 
your system if you use PME (but check the archives - not everybody 
agrees on it).


Osmany Guirola Cruz wrote:

>In last mail i forget do a question... and it's relative to counterions....
>Where can i find information about the role of counterions in MD..
>Should i have to use counterions in all my simulations or depend if i use PME 
>in my simulation or another thing?
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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