GROMACS version: 2022.4
GROMACS modification: No
I have a simulation of a small peptide. I try to make the molecule whole by doing
gmx trjconv -f md_0_1.xtc -s em.gro -pbc whole -o whole.pdb
and choose the protein group.
but this results in some frames with broken molecules (see attached image).
em.gro
itself is not broken. What am I missing?