Center your chosen group within a Gromacs trajectory or structure file effortlessly using the Bai & Breen algorithm.
gcenter can accurately center atom groups, even when they span multiple molecules that may extend beyond the box boundaries. Note that gcenter does not employ connectivity information, so it doesn't require a tpr file as input. However, it also lacks the capability to wrap molecules into the simulation box. Be aware that gcenter exclusively supports orthogonal simulation boxes.
gcenter supports gro and pdb structure files and xtc and trr trajectories and it can autodetect protein residues. Use VMD-like groan selection language to select groups of atoms to center.
0) Install rust.
1) Run cargo install gcenter.
gcenter -c system.gro -f trajectory.xtc -o output_trajectory.xtc
Use gcenter --help for more information about using this program.
Only tested on Linux but should work anywhere.
Only supports orthogonal simulation boxes!