Problem for gmx trjconv

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!

Fixing periodicity effects with gmx trjconv may need multiple invocations and the order of the command matter.
Here is an example of workflow that may help you to solve the problem