[gmx-users] Atoms in radius of X nm (linking atoms in selection by AND not OR)

[Marc Hoemberger]

Thanks for your quick response, I was not aware of this and will have a
look at gmx select!

-Marc

On Thu, Mar 29, 2018 at 8:17 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> This is what the dynamic selections are for, e.g. as implemented in gmx
> select (and some analysis tools).
>
> Mark
>
> On Thu, Mar 29, 2018 at 2:17 PM Marc Hoemberger <hoemberg at brandeis.edu>
> wrote:
>
> > HI Gromacs users,
> >
> > I am trying to count water molecules within 1.5nm of a selection
> residues.
> > Now I know that for a general counting of all water atoms within a radius
> > of a set of atoms I can use trjorder, however what I would like to do is
> to
> > have *only water molecules that satisfy the distance condition for all
> the
> > atoms in my selection*.
> >
> > Is there a way to do such an analysis that I just did not see in the
> > manual, or do I have to use other programs to achieve such a goal?
> >
> > Thanks in advance,
> > Best
> > Marc
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-- 
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453