[gmx-users] g_select, only 'one' water within z>=10 and z<=10.1

[Mark Abraham]

Hi,

If your criterion could satisfy more than one molecule but you for example
only want the first one, then you can likely create a second selection
where you filter out from the first selection the molecule or atom indices
that suit you. I assume that can be done in one call to gmx select, but the
details are an exercise for the reader :-P

Mark

On Fri, 15 Jul 2016 15:52 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> I undrestand my command is not correct for having one water. So it is my
> question how to change the command to have a single molecule?
>
>
>
> Best regards
>
>
> On Fri, Jul 15, 2016 at 3:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/15/16 9:28 AM, Faezeh Pousaneh wrote:
> >
> >> Hi,
> >>
> >> I want to select only a 'single' water molecule at specific part of my
> >> simulation box.
> >> So I try:
> >>
> >> g_select    -selrpos whole_mol_com
> >>
> >> and select
> >>
> >> resname SOL and z >= 10 and z <= 10.1
> >>
> >> But depending on time frame I get more than one molecules or sometimes
> no
> >> molecules. How can I fix it?
> >>
> >>
> > Why do you think that the selection criteria should always return exactly
> > one water?  I see no reason to think that based on what your syntax
> > specifies.
> >
> > -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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