VMD-L Mailing List

From: Aditi Gotkhindikar (aditi.got_at_gmail.com)
Date: Tue Jul 16 2024 - 03:22:20 CDT

Hello,

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,
Aditi