Hi,
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
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
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
