Dear all,
I have a question about salt concentration. I would like to
run a simulation of a protein in an explicit solvent with
a salt concentration of [KCl] = 0.15 mol/L.
My first question is about the neutralization of my protein.
Do I have only to neutralize the global charge of my protein or
do I have to neutralize each charged amino-acid ?
My second question is how do I calculate the number of "extra"
ions I have to put in my system to have [KCl] = 0.15mol/L ?
In fact, I think there are two ways to calculate it.
I can take the volume V of my box given by leap after I solvate my protein
and just use N(K+)=0.15*V/Na
Or I can take the number of water molecules (from the same box) and use
N(K+) = N(water)*O.15/55.555
Does anyone know which method is the one to use ?
Best regards,
Fabien
--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Wed Apr 14 2004 - 15:53:00 PDT
