On Tue, Dec 3, 2013 at 11:14 AM, Stephen P. Molnar
<s.mol...@sbcglobal.net>wrote:
> Thank you for your note. I tried all of the force fields on cyclohexane
> with no change in the structure.
Bear in mind that the conformer resulting from a computational geometry
optimization depends heavily on the starting structure. If the starting
structure is closer to boat, the optimization will follow the gradients to
the stationary point on the PES that corresponds to the boat structure, and
if the starting point is closer to chair, you will get chair. Try moving
some of the atoms to roughly form the chair, and then apply the
optimization. Note that this will happen with Avogadro 1 (or any other
computational code) as well.
Hope this helps,
Dave
> Stephen P. Molnar, Ph.D. Life is a fuzzy
> set
> Foundation for Chemistry Stochastic and
> multivariate
> www.FoundationForChemistry.com
> (614)312-7528 (c)
> Skype: smolnar1
>
>
> -----Original Message-----
> From: Marcus D. Hanwell [mailto:marcus.hanw...@kitware.com]
> Sent: Tuesday, December 03, 2013 10:49 AM
> To: avogadro-discuss@lists.sourceforge.net
> Cc: Avogadro-devel Devel
> Subject: Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released
>
> On Tue, Dec 3, 2013 at 8:25 AM, Stephen P. Molnar <s.mol...@sbcglobal.net>
> wrote:
> > I must say that, in my opinion, this release is premature. I
> > appreciate the comment ' lacks features present in Avogadro 1', but
> > the new version appears to be incapable of rendering benzene as a planar
> molecule at this point.
> > Although the optimized geometry of cyclohexane approximates the less
> > stable boat conformer, the 1.0 version will generate the more stable
> > chair conformer on optimization.
>
> I would disagree, and think that 'release early, release often' is a useful
> mantra in closing the loop between development and use that is employed by
> many open source projects (including Avogadro in the past, and now). We
> worked hard to ensure you could install Avogadro 1 and 2 on the same
> machine, removing any requirement to choose one or the other. Perhaps this
> article will fill add some of the motivation you appear to be inquiring
> about,
>
> http://www.kitware.com/source/home/post/113
>
> When you say 'incapable of rendering' is this referring to the forcefield
> optimization as your second point about cyclohexane is? I am not sure I see
> any reason why a planar benzene would not render, but could see the
> forcefield defaults giving issues. They both use the same forcefields
> underneath (the ones developed by the Open Babel project), and I can look
> into modifying our defaults as I had noticed version 2 generally didn't
> optimize the structures as well.
> >
> > Is it possible that I am missing something in the new, more convoluted
> > directory and subdirectory structure of the gui?
> >
> It is, but you would have to be more specific for me to hope to answer your
> question. If you are just interested in using the Avogadro application I am
> not sure why this would concern you. Thank you for your feedback, if you
> find Avogadro 2 unsuitable then certainly continue using 1.1 for now - we
> have an update planned for that shortly too.
>
> Sincerely,
>
> Marcus
> >
> > -----Original Message-----
> > From: Marcus D. Hanwell [mailto:marcus.hanw...@kitware.com]
> > Sent: Monday, December 02, 2013 2:14 PM
> > To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
> > Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released
> >
> > We are very proud to announce the availability of Avogadro 2 0.7.0.
> >
> > Avogadro 2 is a free, open source, cross-platform molecular editor
> > designed for flexible use in computational chemistry, molecular
> > modeling, bioinformatics, materials science, and related areas.
> > Packages are available for Windows, Linux and Mac OS X. The source
> > code source is available under the 3-clause BSD license.
> >
> > Avogadro 2 is a rewrite of Avogadro, and still lacks features present
> > in Avogadro 1. Both packages can be installed on the same system, and
> > so it is possible to try the latest without losing access to the
> > previous version. We will be making occasional releases of Avogadro
> > 1.x too, along with migrating functionality to Avogadro 2. We value
> > your feedback, and hope that you will find the improvements made in
> version 2 useful.
> >
> > What does Avogadro 2 do?
> > * We've tried to make the best, most intuitive "builder"
> > * Interfaces to many common computational packages
> > * Designed to help both educational users and advanced research
> > * Plugins that allow it to be extended and customized
> > * Can be extended with simple Python scripts for file IO and input
> > generation
> > * Well defined public API, libraries and modular design
> >
> > Download:
> > https://sourceforge.net/projects/avogadro/files/avogadro2/0.7.0/
> >
> > What's new? See the Release Notes:
> > http://wiki.openchemistry.org/Avogadro2_0.7.0
> >
> > For more information: http://wiki.openchemistry.org/Avogadro
> >
> > If you use Avogadro or Avogadro 2, please check out the recently
> > published Avogadro paper, and consider citing it:
> > http://www.jcheminf.com/content/4/1/17
> >
> > This is a community project and we couldn't have made this release
> > without you. Many thanks to all the contributors to Avogadro including
> > those of you who submitted feedback, bug reports, and code. We
> > acknowledge that the development of Avogadro 2 has been funded by a US
> > Army SBIR with the Engineering Research Development Center under
> > contract (W912HZ-12-C-0005) at Kitware, Inc.
> >
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