Is the output really hexagon?

GROMACS version: 2023.3
GROMACS modification: No


I ran a GROMACS simulation using a hexagonal grid. Nonetheless, the resultant .xtc and .tpr files, when opened in Chimera, appear cubic. I checked the input file and it is indeed hexagonal. I cannot determine whether the problem lies in how Chimera visualizes the MD Movie (the actual module name) or if something happened during the simulation.

Or maybe I should try using trjconv?

You need to re-wrap the box with gmx trjconv -pbc mol -ur compact to recover the shape.

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Thanks, so something like this would also be fine given I wish to center it?
printf "1 0" | mpirun gmx_mpi_openmp trjconv -s step7_10.tpr -f step7_10.trr -o step7_10_noPBC.xtc -ur compact -pbc mol -center

Try it and see :)