Hi, 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 ------------------------------------------------ Ran Friedman BitrÀdande Lektor (Assistant Professor)
Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden NorrgÄrd, room 328d http://lnu.se/ccbg ------------------------------------------------ On 9 September 2012 16:10, <gmx-users-requ...@gromacs.org> wrote: > > > Message: 2 > Date: Sun, 9 Sep 2012 13:53:35 +0200 > From: Matthias Ernst <un...@student.kit.edu> > Subject: [gmx-users] genion problem with divalent ions > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <504c833f.2050...@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 > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists