From: Alexandra Ringsby (
Date: Fri May 08 2020 - 16:44:31 CDT

Hi Josh,

Turns out that it was a periodic boundary issue afterall—you're exactly
right, VMD is not pbc aware.

Thanks a bunch!


On Fri, May 8, 2020 at 3:03 PM Josh Vermaas <>

> 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 <>
> 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

Alexandra Ringsby
B.S. Candidate Class of 2021
Chemical Engineering
University of California, Berkeley