VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 08 2020 - 17:56:57 CDT

Hi Alexandra, you may want to try the "pbwithin" keyword instead of
"within".

Giacomo

On Fri, May 8, 2020 at 6:24 PM Alexandra Ringsby <aringsby_at_berkeley.edu>
wrote:

> Hi Josh,
>
> Turns out that it was a periodic boundary issue afterall—you're exactly
> right, VMD is not pbc aware.
>
> Thanks a bunch!
>
> Alexandra
>
> On Fri, May 8, 2020 at 3:03 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
> wrote:
>
>> 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
>>>
>>
>
> --
>
> Alexandra Ringsby
> B.S. Candidate Class of 2021
> Chemical Engineering
> University of California, Berkeley
>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin