[gmx-users] solvation box for say 50mM chaps solution

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Tue Jan 18 14:13:13 CET 2011

HI shahid,
you can also use the following formula
((N_chaps/(Nw*Vw))/6.02214179)*10000=density you want in (Mol) 
- N_chaps is the number of  chaps mol. 614.88 g (from wikipedia)
- Nw : number of water mol. 
- Vw : volume of water (30 A3 in ambiant condition) ~
- 6.02214179 Avogadro number 
- 10000 : correction factor 
I hope this will help

On 18/01/2011 10:33 PM, shahid nayeem wrote:
> Dear Gmx User
> I want to prepare a solvation box for say 50mM chaps solution. The
> density is not known.

An aqueous solution has density close to 1g/mL. That's enough to make an
estimate of the number of molecules, which you can refine if you don't
like the resulting equilibrated size/density/concentration/whatever.


> How should I start calculating the number of chaps molecule and number
> of water molecule required for say 6X6X6 size box, which after
> equilibriation should give the exact strength of the solution. For
> Urea and guanidinium I know the references and mail archive has many
> suggestion but how I should proceed with this new solvation box.
> msnayeem


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