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

Matteo Busato busato.matteo at spes.uniud.it
Wed Dec 20 09:43:52 CET 2017

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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