Trajectory analysis

GROMACS version:2018.7
GROMACS modification: no

Hii everyone !

I need suggestion regarding this weird peak in the attached rmsd graph.

I have done nvt for 5ns and npt for 7ns, and md run for 100ns.while checking the trajectory in vmd, the complex was not exactly within the center of the box, but it is placed on the edge side. In the above attached graph, black one is the protein ligand complex rmsd value.

I am really clueless what I should do to rectify this. I hv also calculated rmsdist, but it is coming properly.

Please help me with any suggestion. I am very new to this field, plz help me to complete the analysis.

This sudden peaks arise because of the periodic boundary conditions. You need to do post-processing of the raw trajectory file to correct the periodic boundary conditions.
Senior Scientist
Quantumzyme LLP, Bangalore