GROMACS version: 2020.3
GROMACS modification: No
I have a homogeneous system of small molecules with Brownian movement in a box size of 5000 x 5000 x 5000 nm. After the simulation, I would like to have the trajectories for molecules that go though a smaller volume (500 x 500 x 1500) inside the box.
How can I print a *.trr file only for the molecules that are inside the smaller volume for each frame? The density of the system should no change. And since the molecules are moving, on each frame I can have different molecules inside de fixed smaller box and I am no sure how to set this.
I tried gmx trjconv with -box but it reduces the whole box and keeps the number of molecules inside it increasing the density.
Any suggestion is greatly appreciated!
Thanks in advance.