Sudden drop in rmsd to zero nm at the end of trajectory

GROMACS version: 2021.3
GROMACS modification: No

Hello gromacs users,

In my backbone rmsd plot below, there is a sudden drop in rmsd to close to zero nm at the end of the trajectory. This is the case for all my rmsd plots. I do not understand this.

Command used: gmx rms -f md.trr -s em.tpr -o rmsd.xvg
Then selected backbone for both LSQ fitting and rmsd calculation

Here em.tpr is the tpr file generated using grompp command for minimization after data collection md run.

Any insight please!


Thank you,

Did you use confout.gro for generating em.tpr? In that case this is exactly what you would expect.


What is confout.gro? I used the following command to generate em.tpr
gmx grompp -f minim.mdp -c md.gro -p -o em.tpr

I tried doing rms analysis using md.gro as reference structure file instead of em.tpr, the rmsd curve looks normal (below)

confout.gro are the final coordinates (and velocities) of your run.

But what did you use as input coordinates to grompp for the case of incorrect RMSD?