Gmx trjconv -pbc whole error

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!

Hi L_k,

just a guess - are you using the tpr file for the -s option when using whole? Otherwise trjconv still gives you a result, but cannot make the structure whole.

Hi cblau,

Thank you for your reply. Yes, I supply the original run tpr file with -s.