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

[Marc Hoemberger]

Hi Mark,

I have been reading the manual (specifically gmx help selections  & gmx
select) and trying to apply the correct syntax in reading out water
molecules that satisfy a defined distance to all of my residues.
The manual states that boolean statements are evaluated left to right and
as soon as the first expression is true the next expressions are not
considered anymore. I would like to couple multiple boolean conditions
together but from the manual this seems to be not possible (unless I might
be misunderstanding something)

I have tried to use the following command:

gmx select -f TRJ.xtc -s TOP.tpr -n INDEX.ndx *-select 'group "OW_WATER"
and within 1.5 of resid 157 and within 1.5 of resid 50' *-os POS.xvg -oi
INDI.dat -on INDEX.ndx

which results in all water molecules around 1.5nm of each individual
residue, I would like to get this expressions to evaluate from left to
right completely so that I only get all those atoms that are within 1.5 of
all the mentioned residues (∧), i.e. not a shortcircuited version. Is this
at all possible, or should I try using other programs/scripts for such an
endeavor.

(Sorry for sending the email twice, I accidentally answered to my own mail)

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