[gmx-users] genion problem with divalent ions

Leandro Bortot leandro.obt at gmail.com
Sun Sep 9 22:37:27 CEST 2012

Hi there,

     In addition to setting -pq to 2 as Justin said, you can set -conc to a
very low value such as 0.00001 for neutralizing the system.

     One more thing... genion apparently uses the box volume when
determining how many ions are necessary for getting a given ionic strength.
 However, depending of your system size and shape and box type the volume
of the protein may be considerable. Maybe the number of water molecules,
instead of the box volume, is a better criterion for determining the number
of ions to be added.

best regards,

2012/9/9 Matthias Ernst <unbyi at student.kit.edu>

> Hi,
> I just encountered (another) strange thing with genion.
> I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
> forcefield amber99sb), so I expected half of the system charge (-52) to be
> added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26
> which would be needed for neutralization. The same holds for Zn or Ca ions,
> which also are divalent in ions.itp
> Could it be that the routines of genion to determine the number of ions
> are not working properly? I mean, the -neutral option also does work only
> if the -conc flag is also there and provides a value > 0.0 (which in fact
> is not what I want when I just want do neutralize my system by adding
> ions...)
> Does anyone of you also had similar problems?
> Thank you,
> Matthias
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