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