[gmx-users] Placing ions at a required distance

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 28 21:26:48 CEST 2011

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.


> Please guide.
> Thanks,
> Shivangi


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


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