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

[Faezeh Pousaneh]

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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