VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri May 08 2020 - 16:02:50 CDT

Hi Alexandra,
Which one is giving more contacts? If it's MDAnalysis, I'd wager that they
are returning contacts across a periodic boundary. VMD's measure contact is
not pbc aware to my knowledge, but MDAnalysis might be. How different are
answers you are getting?
Josh

On Fri, May 8, 2020, 2:54 PM Alexandra Ringsby <aringsby_at_berkeley.edu>
wrote:

> Hello VMD users,
>
> I am using VMD and MDAnalysis to quantify ion association in a
> liquid electrolyte. I have been looking at an atom selection of
> lithium-ions in contact ion pairs in a 50ns MD simulation. I've noticed
> that there is a discrepancy in the number of ions in my VMD selection and
> my MDAnalysis selection. It isn't a python/tcl indexing issue. Are there
> any users of both MDAnalysis and VMD that have experienced inconsistency in
> atom selections? Is it possible that MDAnalysis and VMD have
> different tolerances for the number of atoms in a distance-based selection?
>
> Many thanks,
>
> Alexandra
>