How to Maintain the Integrity of a System Containing Multiple Independent Chains Across PBC in MDAnalysis

[erwushth]

Hi,

I'm currently working on a molecular dynamics simulation project that involves multiple protein chains within the same system. These chains are structurally independent (i.e., no covalent bonds between them) and occasionally span across the periodic boundary conditions (PBC), which complicates the analysis of their interactions and overall structure.

Is there a recommended approach within MDAnalysis to maintain the integrity of independent protein chains that may span PBCs?

Thank you in advance for your time and help!

Best regards,
Wu Shiauthie

[IAlibay]

@erwusht since this is more about usability than a bug, I am transferring this to our discussion forum in the hopes that someone may have a solution for you there.