Fit trajectories (trjconv) issue

User discussions
#1

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

Screen Shot 2021-04-22 at 12.05.57 PM
Screen Shot 2021-04-22 at 12.05.57 PM1978×1598 131 KB

#2

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