[gmx-users] Re: genion problem with divalent ions

ran friedman ran.friedman at gmail.com
Sun Sep 9 18:43:07 CEST 2012

As a side note, you should be careful when using Mg (and probably all other
multiply charged ions, as well as large polarisable ions like I-). It's
very difficult to correctly represent the interactions of such ions in the
bulk correctly using non-polarisable force fields.
Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d

On 9 September 2012 16:10, <gmx-users-request at gromacs.org> wrote:

> Message: 2
> Date: Sun, 9 Sep 2012 13:53:35 +0200
> From: Matthias Ernst <unbyi at student.kit.edu>
> Subject: [gmx-users] genion problem with divalent ions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <504C833F.2050909 at student.kit.edu>
> Content-Type: text/plain; charset="ISO-8859-15"; format=flowed
> 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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