Hello All,
I have been processing some trajectory files by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein appears split in three pieces, and after applying whole there are still two halves. Then, if I apply cluster or nojump there is a clear split down the center of the molecule which seems to be causing an increase in rmsd values. If anyone has experienced this or has a suggestion on how to resolve this, I would greatly appreciate it.
Thank you!