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?
Sorry I did not understood how you did?
First concatenate the trajectory , and then post process with gmx trjconv and finally run gmx rmsd ?
here you find a suggest workflow for gmx trjconv Terminology — GROMACS 2021 documentation
I am facing a similar problem. even if I have the protein looking whole after centering and making it whole via trjconv it still jumps across the box. With my oldtrajcetory the -nojump flag worked pretty fine and solved the issue, but with my new trajectory after applying the nojump flag the trajectory is a complete mess.
So I tried different ways and combinations, but it still does not work. So now I thought of tryinf to frame the nojump flag on an extracted first frame of the trajectory but I actually do not know how to specify this? could you help me?