[gmx-users] surrounding a peptide by ions of magnesium

Justin Lemkul jalemkul at vt.edu
Thu May 2 13:28:50 CEST 2013

On 5/2/13 12:38 AM, Mohan maruthi sena wrote:
> Hi all,
>             I have system consisting of a peptide(alpha-helix), I want the
> peptide to be surrounded by magnesium ions(instead of water). How can i do
> this gromacs? How can I find the concentration of magnesium ions. just like
> in solution we have 0.5 Molar  Mg+2  solution, My question how can  find
> concentration by increasing number of ions.

I don't fully understand what you're trying to do, especially in the absence of 
solvent, but I'll venture some simple advice.  Concentration is just the number 
of moles per unit volume.  Simple unit conversion exercises will tell you how 
many ions are needed to achieve whatever target concentration you're looking for.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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