CCL:G: Overlaying conformers for visualization

[Jan Götze <jgoetze-$-zedat.fu-berlin.de>]

 Sent to CCL by: =?UTF-8?Q?Jan_G=c3=b6tze?= [jgoetze---zedat.fu-berlin.de]
 Dear Andrew,
I suggest using the RMSD Tools you will find in VMD in
 "Extensions"->"Analysis"->"RMSD
 ...". They allow for atom-selective
 alignment of your structures, leading to pretty images of your
 structures and provide the numerical values to quantify your results.
 Best wishes,
 Jan
 Am 26.04.2022 um 19:14 schrieb Andrew DeYoung andrewdaviddeyoung**gmail.com:
>  Hi,
> I'm a postdoc and quantum chemistry novice.  I've run geometry
>  optimization ("Opt") using Gaussian to find several molecular
>  geometries corresponding to local minima on the potential energy
>  surface for a single molecule.  The geometries are similar but not
>  exact.  I'd like to overlay several geometries in order to
>  visualize,
>  qualitatively, how they differ.  In other words I want to overlay
>  multiple conformers.
> Could someone please suggest a relatively simple way to overlay
>  geometries for visualization?  I have access to GaussView,
>  Avogadro,
>  VMD, and any other freeware applications you can think of.  The
>  molecular geometries are in separate .log files (i.e., output from
>  Gaussian), but of course it is easy to convert these to almost any
>  other chemical file format, using Avogadro or the like.
> I realize, though, that "overlaying several conformers" is
>  not a
>  unique specification; one would need to specify which atom(s) to try
>  to overlap exactly.  Is there an algorithm in a computational
>  chemistry program that does this?
>  Thank you for any guidance you can provide!
>  Andrew
>  Andrew DeYoung, PhD
>  Department of Chemistry
>  Carnegie Mellon University
 --
 ----------------------
 Dr. Jan Philipp Götze
 Quantum Chemistry of Biological Systems
 Institut für Chemie und Biochemie
 Freie Universität Berlin
 https://jgoetze.userpage.fu-berlin.de
 Currently only home office due to Corona restrictions