GROMACS version: 2023.1
GROMACS modification: Yes/No
When I use gmx trjconv to remove pbc and rot+trans on a trajectory, the new xtc trajectory shows a sudden dramatic shift in the atomic coordinates of some frames. To put it figuratively, imagine a movie where a person is walking, and at some point in the movie the person is upside down. But for the most part, the person walks normally.
I looked at the raw xtc trajectory using VMD and this problem did not arise. Only after I using command “gmx trjconv… -fit rot+trans” or “gmx trjconv… -pbc mol-center -ur compact”, this happens and no errors are reported.
Hope to get some help, thanks!