[gmx-users] Dynamic selection of a shell in a trajectory
mark.j.abraham at gmail.com
Wed Dec 20 11:33:55 CET 2017
Dynamic selections are implemented, but only for a small subset of GROMACS
tools. You can use gmx select to form the appropriate index group, but
you'd have to write some other script to get trjconv to pull out individual
frames with the matching selection, and then concatenate them into a
trajectory file (and decide how you want to deal with the fact that frames
may now differ in the number of atoms).
On Wed, Dec 20, 2017 at 9:03 PM João Henriques <joao.m.a.henriques at gmail.com>
> 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
> > the metal, e.g. say to the system "consider a sphere of 8 Angstroms
> > 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
> > 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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