From: Vermaas, Josh (
Date: Tue Jul 16 2024 - 06:18:47 CDT

My usual advice is to center on *one* monomer, rather than on the whole protein. For the few frames where the dimer jumps across a pbc edge, the center of mass of the protein will be somewhere in solution.


From: <> on behalf of Aditi Gotkhindikar <>
Date: Tuesday, July 16, 2024 at 5:36 AM
To: VMD Mailing List <>
Subject: vmd-l: PBC issue


I am working on a 100 ns simulation trajectory file of a dimer protein (NAMD) and facing a pbc issue.
1. When the trajectory is loaded on the psf, the chain A and B of the dimer protein are stable for the first half of the simulation. But later they get separated for a few frames in between and again join back.
commands used for this - pbc wrap -center com -centersel "protein " -compound residue -all

2. But now the chains are getting mixed into one another. They are interlocked in one another for a few frames in the second half of the simulation.

Please let me know a solution to solve this and have a smooth trajectory.

Thank you,