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

Mark Abraham mark.j.abraham at gmail.com
Thu Mar 29 14:18:07 CEST 2018


This is what the dynamic selections are for, e.g. as implemented in gmx
select (and some analysis tools).


On Thu, Mar 29, 2018 at 2:17 PM Marc Hoemberger <hoemberg at brandeis.edu>

> 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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