From: Benjamin Bouvier (benjamin.bouvier_at_ibcp.fr)
Date: Wed Jul 22 2009 - 16:25:40 CDT
Rabab,
You can compute the volume of the periodic box from its spanning vectors,
which are reported by NAMD. Convert that volume into liters. Convert the
protein quantity of substance into moles by dividing the number of units
in the box (usually 1) by the Avogadro number. Divide both figures to get
the molarity in mol/L.
Benjamin Bouvier.
On Wed, 22 Jul 2009 22:16:58 +0200, Rabab Toubar <rtoubar_at_yahoo.com> wrote:
> Hi,
>
> I was wondering if there is a way to measure the molarity of the
> solvated protein using NAMD or VMD
>
> Thanks
>
> Rabab Toubar
>
>
>
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