[gmx-users] counterions?

Ran Friedman ran at hemi.tau.ac.il
Sun Jul 16 18:57:05 CEST 2006


If you want to add ions near charged residues and want to know how much, 
just count the number of charged residues, and add one positive and one 
negative charge for the N- and C- termini.
You can use g_sas to locate the solvent-exposed residues if that's needed. 

However, I think that no matter where you put the ions, they will 
relocate once the simulation equilibrates. So it may be better just to 
put enough ions to neutralise the system. You can then add some ions to 
reach the desired ionic strength. genion can be used to randomly put the 
ions in place, which makes sense since they're very mobile anyhow.

Hope that helps,

Samuel C Flores wrote:

>Hi Guys,
>Can anyone tell me how I should go about adding counterions in GROMACS?
>Right now I am adding just enough counterions to make the net charge equal
>to zero.  However I believe I should be adding a counterion for each charged
>atom on the surface, according to some algorithm.  Is there some program out
>there, similar to Amber's CION, for deciding how many counterions to supply?
>I think I can use genion to actually place them, right now I just want to
>know how many I need..
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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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