From: Efthymiou, Christos (
Date: Fri Apr 28 2023 - 01:58:28 CDT


I am trying to calculate the RMSD for each frame in my simulation, but I noticed that there are two sections near the end (around 100-200 frames each) where the RMSD suddenly jumps from around 2 to 6 angstroms. I have visualized a portion of the trajectory and it appears that the protein-protein complex is partially crossing the periodic boundary condition and causing this issue. In my script, I have used the command pbc wrap -centersel "protein" -compound residue -all prior to calculating the RMSD. I have also tried using pbc unwrap -sel "protein" -all first, but the issue persists. I also tried having the pbc wrap command happen again 25%, 50%, and 75% of the way through the calculation by placing it within the RMSD calculation loop with an interval, but this still did not solve the issue.

How can I ensure that my RMSD calculation is corrected, and the protein-protein complex does not cross the periodic boundary condition if pbc wrap is not working?