[gmx-users] genion problem with divalent ions
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
Does anyone of you also had similar problems?
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