VMD-L Mailing List

From: Roni Saiba (ronis_at_imsc.res.in)
Date: Thu Dec 21 2023 - 01:05:23 CST

We have run polymer simulations in LAMMPS in which we have added bonds
between crowder particles and specific monomers based on a distance
criteria. When loading the .trj file in VMD I am loading a .psf file
of the initial configuration. As a result the newly added bonds are
not visible. Using dynamic bonds shows bonds between particles which
can not have a bond. I have written a script which saves .psf files at
different files and load the frames as different molecules. Is there a
way to load .psf files dynamically for easier visualization?

Regards,
Roni Saiba
IMSc Chennai