Thank you for your note. I tried all of the force fields on cyclohexane with no change in the structure.
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. > > ---------------------------------------------------------------------- > ------ > -- > Rapidly troubleshoot problems before they affect your business. Most > IT organizations don't have a clear picture of how application > performance affects their revenue. With AppDynamics, you get 100% > visibility into your Java,.NET, & PHP application. 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