[gmx-users] calculation of concentration

[Tsjerk Wassenaar]

Hi Sara,

1 M = 1 mole / dm^3 = 6.022e23 molecules / dm^3
(6.53 nm)^3 = 6.53e-8^3 nm^3
Concentration: 60 / 6.022e23 / 6.53e-8^3 = 0.3578

Alternatively, you can work with the number of solvent molecules

1L H2O = ~55.4 mole
1M = 1 molecule / 55.4 molecules H2O
Concentration = 60/(7579./55.4) = 0.4386

The discrepancy between the methods is due to the small volume/amount.

Hope it helps,

Tsjerk







On Thu, Dec 22, 2011 at 6:44 PM, mohammad agha <mra_bu at yahoo.com> wrote:
> Dear GROMACS users
>
> I doubt about calculate the concentration of my system. I know that
> concentration is calculated from the number of molecules / Avogadro’s number
> and divided by volume of box, but I think I calculate wrong, for example in
> one of articles had been written:
> 7579 water molecules + 60 SDS molecules (surfactant with anionic headgroup)
> + 60 Na ion (with a positive charge) in the cubic box with box size = 6.53
> nm , has concentration = 0.4 M.
>
> May I know how do you calculate this, please?
>
> Best Regards
> Sara
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands