From: Vermaas, Josh (
Date: Fri Apr 28 2023 - 04:20:23 CDT

Hi Christos,

If you have a protein complex that is split apart by PBC, you need to put it back together again for RMSD analysis. pbc unwrap is supposed to do this, but may run into issues if there are any frames that do not have periodic box information loaded into them. Trajectory files like dcds or xtcs have these by default, but not all inputs do. Another thing to try is to PBC wrap around *one* of the protein domains. That declares that one domain is the "center", and the algorithm will try and put everything within 1 box of that central protein. If you select over the whole "protein" selection, the center of the selection will be the center of mass of the separated proteins, which is probably in solution somewhere, and isn't what you want.


On 4/28/23 02:58, Efthymiou, Christos wrote:

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?


Josh Vermaas<>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University