GROMACS version:gromacs/2018.3
GROMACS modification: Yes/No
Dear all,
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?
Thanks!
Best,
Juliana
Hi,
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
Best regards
Alessandra
Hi there!
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?
