GROMACS modification: Yes/No
I’m trying to fit my trajectory using the command trjconv however my rmsd is showing jumps at the times where my trajectories were connected to each other (at 30 and 60ns). I already tried to use different strategies
-pbc no jump, then -fit rot+trans,
-pbc mol -center, then -fit progressive
I tried also to create the file for the first frame of the trajectory and run trjconv -fit rot+trans using -s firstframe, but my RMSD graph is still showing jumps on 30ns and the biggest is at 60ns.
I also extracted the frames at different times (beginning, middle, end) of the trajectory and they look properly aligned on chimera.
Does anybody know how to fix this fitting issue?