# Issues when using -fit rot+trans **URL:** \ **Category:** User discussions\ **Created:** [June 6, 2024, 10:03am UTC](https://gromacs.bioexcel.eu/t/issues-when-using-fit-rot-trans/9323 "2024-06-06T10:03:45Z")\ **Posts on this page:** 1\ **Showing post:** 5
**Author:** ![abelxf](https://avatars.discourse-cdn.com/v4/letter/a/cdc98d/32.png) [@abelxf](https://gromacs.bioexcel.eu/u/abelxf)\ **Post date:** [June 8, 2024, 3:41pm UTC](https://gromacs.bioexcel.eu/t/issues-when-using-fit-rot-trans/9323/5 "2024-06-08T15:41:09Z")
Dear @obZehn The steps I had followed for pbc removal prior to use of -fit rot+trans are 1. gmx trjconv -pbc whole (The protein was broken across the box) 2. gmx trjconv -pbc mol -center (The protein was at the edge of the box after -pbc whole) 3. gmx trjconv -fit rot+trans (The protein was rotating around a lot, hence messing up downstream analysis) Before applying fit rot+trans, no part of my protein was leaving the box. It was safely confined to the center, but rotating a whole bunch. Since for the algorithm I am using to find the group of water molecules of my interest require the protein to be aligned to the z axis(in this case, to the .tpr file), I had to align the trajectory. Does that seem fine? Thanks a lot for your time --- _[View the full topic](https://gromacs.bioexcel.eu/t/issues-when-using-fit-rot-trans/9323)._