Hi
I am using Gromacs 2018 version. I ran the MD simulation for 400 ns at 300K (I didn't change the classic tutorial md.mdp except for nstep). While watching the .xtc file, I noticed that the water molecules were coming out of the simulation box, but I ignored it (image 1 is the figure I saw in frame 0, while image two further frames). I thought it wouldn't be a problem because of PBC, but I still couldn't understand why it was like this. What surprised me was that at 400 ns, there were no ions left in the unit cell and ions were visible outside the unit cell. According to PBC, if an ion was leaving the unit cell (it must have left since I saw ions around it), wouldn't the ions have to come back in to balance the number of molecules inside? It's as if there are no ions in my unit cell but there are ions in the display cells. How is this interpreted? Any idea what is the problem?
Try the trajconv (gromacs knife) for centring the macromolecule and then analyze for RMSD and RMSF for molecule of interest i.e. protein or ligand.
I hope that might work for you.