From owner-chemistry@ccl.net Tue Apr 26 21:49:00 2022
From: "Andrew DeYoung andrewdaviddeyoung**gmail.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL:G: Overlaying conformers for visualization
Message-Id: <-54648-220426131509-22964-R0uJMP4+b0vJ5UAmDkAhgw^^^server.ccl.net>
X-Original-From: Andrew DeYoung <andrewdaviddeyoung-x-gmail.com>
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Date: Tue, 26 Apr 2022 13:14:52 -0400
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Sent to CCL by: Andrew DeYoung [andrewdaviddeyoung::gmail.com]
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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

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<div dir=3D"ltr">Hi,<div><br></div><div>I&#39;m a postdoc and quantum chemi=
stry novice.=C2=A0 I&#39;ve run geometry optimization (&quot;Opt&quot;) usi=
ng Gaussian to find several molecular geometries corresponding to local min=
ima on the potential energy surface for a single molecule.=C2=A0 The geomet=
ries are similar but not exact.=C2=A0 I&#39;d like to overlay several geome=
tries in order to visualize, qualitatively, how they differ.=C2=A0 In other=
 words I want to overlay multiple conformers.</div><div><br></div><div>Coul=
d someone please suggest a relatively=C2=A0simple way to overlay geometries=
 for visualization?=C2=A0 I have access to GaussView, Avogadro, VMD, and an=
y other freeware applications you can think of.=C2=A0 The molecular geometr=
ies 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.</div><div><br></div><div>I realize, though, that &qu=
ot;overlaying several conformers&quot; is not a unique specification; one w=
ould need to specify which atom(s) to try to overlap exactly.=C2=A0 Is ther=
e an algorithm in a computational chemistry program that does this?</div><d=
iv><br></div><div>Thank you for any guidance you can provide!</div><div><br=
></div><div>Andrew</div><div><br></div><div>Andrew DeYoung, PhD</div><div>D=
epartment of Chemistry</div><div>Carnegie Mellon University</div></div>

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