[gmx-users] Ionic strength

[Santi Esteban Martin]

Dear gmx,

I would like to fix the Ionic Strength of a system of a protein
in water (at a particular pH !!! ).

Experiemntally, one fix it (i.e I = 0.1M) taking into account buffer 
and salts but not protein protonation state, for instance(is it true?).

When calculating it 

 I= SUM( charge**2 * Concentration ) 

for a simulation, should I achieve i.e. I= 0.1 
taking into account only ions or one should include the total charge
of the protein and ions concentration in the equation ?
(oops!! and carefully setting neutral solution ;-) )

If one must take into account the macroion(protein) when computing "I",
so my thoughts are :

calculate protein PKAs (whatif-delphi) using I = 0.1(i.e.)
Look the charge of my protein at my PH
Achieve the Ionic Strentgh adding ions without forgetting  the 
protein contribution.

Problem : if at particular pH your protein has lot of total charge, 
the only solution to decerase the ionic strentgh is to increase 
the Volume but that not sound good idea.


What are your ideas ?

Thanks a lot
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