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

[Mark Abraham]

Hi,

"The first molecule found with Z between these values" seems perfectly well
defined to me. I haven't checked how one might implement it, though.

Mark

On Mon, 18 Jul 2016 11:31 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> Thanks Mark, but I hardly believe that helps. What you suggest can work for
> only one frame. But I need a selection which works at the same time for all
> frames (in my loop over trajectory), where there are no molecules at some
> frames or two or more at others (in z >= 10 and z <= 10.1).
>
>
> Best regards
>
>
> On Fri, Jul 15, 2016 at 6:48 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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