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