[gmx-users] counterions?

Samuel C Flores samuel.flores at yale.edu
Sun Jul 16 21:39:43 CEST 2006



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?    





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?



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
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