[gmx-users] Placing ions at a required distance

[Justin A. Lemkul]

shivangi nangia wrote:
> 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.
> 

Are these ions simply going to be part of the bulk solution?  If so, use genion. 
  Manual intervention is not necessary since random initial velocities will 
disrupt any sort of idealized geometry that you construct.

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

Yes and no.  If you really believe you need a specific location of a Li+ ion in 
your simulation cell, either (1) write a simple .gro file by hand and 
concatenate it with the coordinate file of your other system components or (2) 
use editconf -center to define its coordinates and concatenate that file with 
your system.  Li+ parameters should be present in ions.itp for most force 
fields, so just #include that topology like you would any other system.

-Justin

> Thanks,
> Shivangi
> 
> 
> 
> On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

========================================