[gmx-users] genion problem with divalent ions

Justin Lemkul jalemkul at vt.edu
Sun Sep 9 14:42:19 CEST 2012

On 9/9/12 7:53 AM, Matthias Ernst wrote:
> 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

Charge is not read from ions.itp, it is taken from the command line.  The value 
of -pq is 1, so if you're adding divalent metals, set it to 2.

> 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...)

This has been an issue for a long time.  I suppose no one has ever filed a 
redmine issue for it, so please do.  Otherwise, it won't get fixed.



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


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