[gmx-users] genion

Kalyan Reddy modugulas at gmail.com
Fri Mar 14 10:02:35 CET 2014

Dear Andrew,

First of all you just have a look at the "*Ions.itp" *file, which exists in
"gromacs-4.5.2/share/top/(any forcefield you are working with)" in your
installed directory.

There you will find all types of *Ions* we can use.

Regarding *genion tool, *this command should work:

"*genion -s ions.tpr -o Solv_ions.gro -p topol.top -pname ZN -np 5"   *------
   for random placement of ions

"*genion -norandom -s ions.tpr -o Solv_ions.gro -p topol.top -pname ZN -np
5"  *  -------      for placing ions base on potential

All the Best.

On Fri, Mar 14, 2014 at 1:43 PM, Andrew Bostick
<andrew.bostick1 at gmail.com>wrote:

> Dear gromacs users
> In genion tool of gromacs, there are only Na and Cl ions. I want to add
> Zn2+ ions to my system.
> How to add these ions with special concentration?
> Any help will highly appreciated
> --
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Kalyan Reddy

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