Hii everyone, I have performed md simulation of a protein ligand complex using gromos54-a7 force field. I have done nvt for 5ns and npt for 7ns and md run for 100 ns. Then while analysing trjconv the command I have used - gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center
… used protein for centering and system for output.
nxt calculate rmsd.
Here I am attaching my rmsd picture- black is protein-ligand complex, red for ligand , green for protein.
I am very new to this field. I donot understand what optimisation or correction I need to do.
