VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 03 2024 - 13:04:34 CST

For DynamicBonds to work the way you expect, it may be necessary to combine
multiple representations with different atom selections and bond cutoffs.
Please also note that atoms that would be detected as hydrogen atoms (you
will have to assign atom and element names accordingly after loading and
call `mol reanalyze`) will only form bonds to other elements and thus you
can use that to remove unwanted bonds as well.

VMD does not support combining and switching between different bond
topologies, so to make this work you would have to do extensive scripting
that is specific to your system.

If you create a different .psf file for each frame, you could use the multi
molecule animation extension:
https://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/

On Thu, Dec 21, 2023 at 3:52 AM Roni Saiba <ronis_at_imsc.res.in> wrote:

> 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
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!8Fi5ZdZotA-ggsoqNS12j1agi40kqSMxUdkvFbeDqXIebcNsLdb7i-xlApWB561Aki8X2nBhA-Vw-tpefg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA