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

[Mohan maruthi sena]

Hi ,
        Thanks for a quick reply. Sorry for not being clear,  I want to
surround the peptide with just ions(sodium). How can I  do this?

Thanks,
Mohan


On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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