[gmx-users] Usually how do you decide the salt concentration?

[Justin A. Lemkul]

Peggy Yao wrote:
> Dear all,
> 
> Usually how do you decide the salt concentration of the system?
> 

The salt concentration depends on a realistic physical model of whatever system 
you're examining.  Note that in real biological systems, "salt" is a very broad, 
complex concept, so some approximations will have to be made.

> I got a protein structure from PDB, and what I am doing now is: to find 
> out from which species the protein is extracted, and then search in 
> google for the normal salt concentration of that species. However, it's 
> hard to find the normal salt concentration.
> 

Well, then you've got your work cut out for you.  Google is not the be-all 
end-all of information.  Certainly there are studies using that particular 
organism, or at least some that are similar, about which more information is known.

In the absence of information about the organism itself, search for whether or 
not assays have been performed on your protein that are involved in the behavior 
you hope to simulate.  Those buffer conditions may be relevant to your simulations.

-Justin

> I will appreciate if you can share with me how you decide what the salt 
> concentration. Thanks!
> 
> Peggy
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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