Dear @obZehn
The steps I had followed for pbc removal prior to use of -fit rot+trans are
- gmx trjconv -pbc whole (The protein was broken across the box)
- gmx trjconv -pbc mol -center (The protein was at the edge of the box after -pbc whole)
- 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