[gmx-users] Placing ions at a required distance

[shivangi nangia]

Hi again,

I did not quite understand the suggestion.
I have successfully added Li+ ions in my simulation box using genion.
I am confused about how to place Li+ ions using editconf.

Will I have to create a .gro and .itp file and add it like a solute ?

Thanks,
Shivangi



On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shivangi nangia wrote:
>
>> Hello,
>>
>> I am a new gromacs user.
>>
>> I want to place Li+ ions at a required distance from the polypeptide (
>> which is at the centre of a box of water)
>>
>> I searched through the archive and the manual if there is a way/provision
>> to do this, but could not.
>>
>> Is there a way?
>>
>
> Measure the distance you want and establish the coordinate at which you
> wish to place the ion, then use editconf -center to place it at the proper
> location in the simulation box.
>
> -Justin
>
>
>>
>> Please guide.
>>
>> Thanks,
>> Shivangi
>>
>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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