AMBER Archive (2004)

Subject: AMBER: salt concentration

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Wed Apr 14 2004 - 09:45:44 CDT

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_at_ibpc.fr
IBPC    13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________

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