[gmx-users] counterions?

[Ran Friedman]

I guess the ionic strength is solution (0.1-0.15M) would do it. As the 
number of ions near the protein surface changes during the simulation, I 
don't think you can say much about the ionic strength near the protein.

Ran.

Samuel C Flores wrote:

> Hmm..
>
>  
>
> Well counting the charged residues leads to scores of ions, which I 
> think would be a tight squeeze in my water box, given that each ion 
> should have a hydration shell around it.  
>
>  
>
> I like the idea of neutralizing, then adding ions to reach a certain 
> ionic strength.  However how to know exactly what ionic strength I 
> need?  I am modeling murA, but haven't found an ionic strength in the 
> literature.  Also, wouldn't the ionic strength near the protein be 
> different from that elsewhere in the solution?    
>
>  
>
> Sam
>
>  
>
> ------------------------------------------------------------------------
>
> *From:* gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Ran Friedman
> *Sent:* Sunday, July 16, 2006 12:57 PM
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] counterions?
>
>  
>
> Hi,
>
> 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,
> Ran.
>
> 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..
>
> 
>
> 
>
> 
>
>Sam  
>
> 
>
> 
>
> 
>
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>-- 
>
>------------------------------------------------------
>
>Ran Friedman
>
>http://bioinfo.tau.ac.il/~ran <http://bioinfo.tau.ac.il/%7Eran>
>
>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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-- 
------------------------------------------------------
Ran Friedman
http://bioinfo.tau.ac.il/~ran
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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