[gmx-users] genion problem with divalent ions

Matthias Ernst unbyi at student.kit.edu
Sun Sep 9 13:53:35 CEST 2012


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,

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