[gmx-users] genion -conc give the wrong number of multi-valent counter ion

[Mark Abraham]

Hi,

In general, run "gmx help tool" to see how the tool should be run, here to
see that there's an option for you to choose a non-default charge

Mark

On Fri, 16 Jun 2017 14:21 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/16/17 7:14 AM, Quyen V. Vu wrote:
> > Dear GMX developer,
> > I don't know this mailing list is suitable for posting issue or not, if
> > not- forgive me.
> >
> > I want to report about gmx genion module
> >
> > If i want to add concentration of salt by -conc option, it just correct
> for
> > monovalent salt (eg. NACL).
> >
> > For multivalent salt(MGCL2), if I use -pname MG -nname CL -conc X
> -neutral
> > , it wil treat MG as monovanlent cation and give the wrong number of ions
> > add into my system, so  I have to use -np and -nn option to get correct
> the
> > number of ions.
> >
>
> If you set the correct value of -pq then you'll get the right result.
> genion
> defaults to assuming everything is monovalent and if that's not the case,
> you
> have to provide correct instructions via the command line.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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