[gmx-users] Dynamic selection of a shell in a trajectory

João Henriques joao.m.a.henriques at gmail.com
Wed Dec 20 11:02:46 CET 2017

Very unlikely and/or impractical. The water selections/analyses you can do
with gromacs' native tools are unfortunately rather limited. From personal
experience I'd suggest trying MDAnalysis or something similar, because it
gives you the freedom to code your our analysis routine with minimal effort
in terms of programming. Plus it allows dynamic selections, which I never
found truly possible with gromacs' native tools.


On Wed, Dec 20, 2017 at 9:43 AM, Matteo Busato <busato.matteo at spes.uniud.it>

> Dear all,
> I'm performing a dynamic of a metal ion in a box consisting of a solvent,
> where the metal is coordinated by six solvent molecules.
> I'm writing here because I want to reduce the trajectory including the
> intire box to a trajectory containing only the first coordination shell of
> the metal, e.g. say to the system "consider a sphere of 8 Angstroms radius
> from the metal and pick up any residue which has a least one atom inside
> this sphere". In addition, it would be nice to perform a sort of "dynamic
> selection", e.g. if one residue exits and another one enters the sphere I
> want the selection to keep the first one and then the second.
> Is this possible with Gromacs or do I need to use other tools? I've tryed
> to understand if this was possible with trjconv or gmx select, but I think
> they're not the right utilities and I couldn't find anyone with this
> problem in a web research.
> I would be gratefull if you can help me.
> Thank you in advance for your answer.
> Kind regards,
> Matteo Busato
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