[gmx-users] adding a negative two charged ion

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 15 16:50:53 CEST 2009

CandyCandy wrote:
> Dear gromacs users,
> I am using genion command to add a negative two charged ion:
> genion -s water.tpr -o watern.gro -nq 2 -nname O- -nn 1 -g watern.log.

Well, "-nq 2" will set a charge of +2, not -2.

> It does not work. It shows:
> Fatal error: No such moleculetype O
> Could anybody give me some idea about making a -2 charged ion? Thank you so
> much!

Probably because such a species does not exist within the force field you're
trying to use.  Check out ions.itp for existing ion types.  If you have to
create a new species, you have the very difficult task of parameterization ahead
of you:



> Best regards,
> Candy 
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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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