I have to simulate protein in 400mM calcium ion conc. I will neutralise the system with chloride ions.
My system now has 265 protein residues and 18610 water (SPC) molecules. How many calcium do I need to add to make the ion conc of 400mM? Also let give me a detailed calculation for my understanding. Also state number of chloride ions required to neutralise the system (total charge of system currently is -12)
Lets do first consider a 400 mM calcium ions.
The Molarity or molar concentration is defined as:
c_i = n_i/V = N_i/(N_A*V).
If we neglect the excess volume due to the electrolyte,
we can express it as:
V = N_H2O * M_H2O / (\rho_H2O * N_A).
Now we can substitute V in equation 1 with eq.2 and rearrange:
N_i = M_H2O * M_H2O * c_i / \rho_H2O
For simplification we assume a density of 1 g/cm3,
and we get for the number of Ca2+:
18610*18*(g/mol)*0.4*(mol/dm3)/(1*g/cm3) = 133.992
which is approx. ~ 134 ions.
If the total charge of your system is now (without ions) -12 then
simply add 134 Ca2+ and 256 Cl- to get charged neutralized system,
because
(134*2)-256-12=0 !
http://manual.gromacs.org/online/genion.html
U can neutralize as well as can use a specific conc. of salt by doing this.
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