VMD-L Mailing List

From: Alexandra Ringsby (aringsby_at_berkeley.edu)
Date: Fri May 08 2020 - 15:22:28 CDT

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