High RMSD value and Fluctuations – User discussions

GROMACS version: 2019.3
GROMACS modification: No

Dear all,

I know that there are lots of topics about high RMSD value, sudden jumps or fluctuations. I’ve been scrolling through the topics and trying to apply several trjconv commands into my system but could not even get a smooth RMSD value and I am not sure if my system has crashed. I have carried out protein+ligand MD simulation and I had smooth RMSD values so far except the last system I set up for my simulation. I couldn’t fix my RMSD result even though I have tried several commands that I have listed out of order.

gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -center -pbc mol

trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_fit-rot_trans.xtc -ur compact -fit rot+trans

gmx trjconv -s prod_md.tpr -f prod_md.xtc -o prod_md_nopbc_cluster.xtc -pbc cluster

Sadly, these commands did not work, I think I am missing some points since I’m new to GROMACS. Sorry for bringing this topic up again but I got quite confused.

Here is the RMSD result of my system:


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