## avogadro-discuss — General discussion for users of Avogadro

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 Re: [Avogadro-Discuss] Vibration animation and molecular database... From: Roy Jensen - 2010-12-27 06:05:45 Attachments: H2O.g03 ```Geoff In the H2O output file, attached, the second (of ten) settings has the hydrogen atoms disappearing into the oxygen atom. Every higher setting has the hydrogen atoms appearing out the other side! Vibrations at the third or higher setting leads to inversion and hydrogen overlap. In a classical approximation, the hydrogen atom, which moves the most, moves a maximum of 14 % of the bond length. I am not sure how you are calculating the displacement, but a range from 5 % to 50 % of the bond length would be great (from around 5 pm to 75 pm). My calculation of the displacement is given below: In classical physics, Hookes law gives 2 * pi * v = SQRT(k/m) Energy is given by E = 1/2 * k * x^2 = h * v Solving Hookes law for k and substituting into the energy equation gives x^2 = h/(2 * pi^2 * m * v) For hydrogen in water at 4000 cm-1, x is 13 pm, which is 14 % of the 95 pm bond length. (m should really be the reduced mass. But then again, this is an application of _classical_ physics to a _quantum_ system.) The above classical calculation is a reasonable approximation of the turning points on the OH PES: for a bond length of 97 pm, the first vibrational energy level turning points are at 82 and 119 pm, corresponding to -15 pm and +22 pm. Thanks, Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan University Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 On Fri, 24 Dec 2010 17:50:19 -0500, you wrote: > >On Dec 22, 2010, at 5:27 AM, Jan Halborg Jensen wrote: > >>> That said, I noticed that the animate feature of Avogadro *wildly* >>> exaggerates the vibrational motion. The lowest setting is actually >>> about 10 times greater motion than in reality! > >I'm always open to suggestions. I generally use a "wildly" exaggerated vibrational motion because I find in lecture demonstrations that 2x or 3x is not usually sufficient for students to understand the modes. They see that the atoms are moving, but have a difficult time differentiating the direction of movement. So I often find myself cranking it up to 20-30x... > >Maybe you have smaller lecture halls? > >It's obviously a *very* easy patch. Just give me some feedback on what you think the slider ranges should give. > >> I agree: it would be very educational to have an option where the >> displacements were properly scaled according to frequency: >> http://molecularmodelingbasics.blogspot.com/2010/06/geometry-and-molecular-motion.html > >Jan, I don't recall you giving this suggestion before -- we previously changed the speed of vibration to scale according to frequency, and it's again a fairly trivial patch. (Easy enough, I suspect you or one of your students could submit it) > >While Quixote is definitely the way to go for a computational repository, I'm also happy to host a repository of "good teaching examples" on the Avogadro website in whatever file format is desired -- it need not be CML, since Avogadro can read such a wide range. > >-Geoff > > >------------------------------------------------------------------------------ >Learn how Oracle Real Application Clusters (RAC) One Node allows customers >to consolidate database storage, standardize their database environment, and, >should the need arise, upgrade to a full multi-node Oracle RAC database >without downtime or disruption >http://p.sf.net/sfu/oracle-sfdevnl >_______________________________________________ >Avogadro-Discuss mailing list >Avogadro-Discuss@... >https://lists.sourceforge.net/lists/listinfo/avogadro-discuss ```
 Re: [Avogadro-Discuss] Vibration animation and molecular database... From: Geoffrey Hutchison - 2010-12-25 14:31:53 ```On Dec 22, 2010, at 5:27 AM, Jan Halborg Jensen wrote: >> That said, I noticed that the animate feature of Avogadro *wildly* >> exaggerates the vibrational motion. The lowest setting is actually >> about 10 times greater motion than in reality! I'm always open to suggestions. I generally use a "wildly" exaggerated vibrational motion because I find in lecture demonstrations that 2x or 3x is not usually sufficient for students to understand the modes. They see that the atoms are moving, but have a difficult time differentiating the direction of movement. So I often find myself cranking it up to 20-30x... Maybe you have smaller lecture halls? It's obviously a *very* easy patch. Just give me some feedback on what you think the slider ranges should give. > I agree: it would be very educational to have an option where the > displacements were properly scaled according to frequency: > http://molecularmodelingbasics.blogspot.com/2010/06/geometry-and-molecular-motion.html Jan, I don't recall you giving this suggestion before -- we previously changed the speed of vibration to scale according to frequency, and it's again a fairly trivial patch. (Easy enough, I suspect you or one of your students could submit it…) While Quixote is definitely the way to go for a computational repository, I'm also happy to host a repository of "good teaching examples" on the Avogadro website in whatever file format is desired -- it need not be CML, since Avogadro can read such a wide range. -Geoff ```
 Re: [Avogadro-Discuss] Vibration animation and molecular database... From: Peter Murray-Rust - 2010-12-22 11:33:23 Attachments: Message as HTML ```On Wed, Dec 22, 2010 at 11:00 AM, wrote: > >> On a second note, has there been thought to provide a database of > >> ground state molecules, with IR and NMR spectra for the smaller > >> entities? This would be valuable for the average user, who doesn't > >> have access to computational software and/or doesn't know how to use > >> computational software. > If you are interested in experimental data then there is http://wwmm.ch.cam.ac.uk/crystaleye with 200,000 crystal structures and nmrshiftDB (http://www.ebi.ac.uk/nmrshiftdb/ ) for NMR shifts I am not aware of much for IR except NIST webbook I think's its a good idea to provide both expt and calculations as then each helps to calibrate and encourage the other. -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 ```
 Re: [Avogadro-Discuss] Vibration animation and molecular database... From: - 2010-12-22 11:00:27 ```>> On a second note, has there been thought to provide a database of >> ground state molecules, with IR and NMR spectra for the smaller >> entities? This would be valuable for the average user, who doesn't >> have access to computational software and/or doesn't know how to use >> computational software. >> >> So, my questions for everyone: >> * is a molecular database a good idea? >> * is it something that can be hosted on Avogadro.net? >> * how should it be done? what format should be adopted? > >I believe this is within the scope of the Quixote project: >http://quixote.wikispot.org/Front_Page It is, and Avogadro is fingered as the code that we intend to do most of our prototyping of querying/accessing the database with, so with any luck, it shouldn't be too long before there is something people can try. Best wishes, Jens -- Scanned by iCritical. ```
 Re: [Avogadro-Discuss] Vibration animation and molecular database... From: Jan Halborg Jensen - 2010-12-22 10:27:44 ```"Roy Jensen" skrev: > > A colleague asked if In knew of any software for animation of > molecular vibration. (She has explained that she would be flapping her > arms in class if I didn't know of any ... and I am seriously thinking > about claiming ignorance and installing a camera.) > > That said, I noticed that the animate feature of Avogadro *wildly* > exaggerates the vibrational motion. The lowest setting is actually > about 10 times greater motion than in reality! The higher settings > actually see the atom vibrate through the molecular geometry! Perhaps > the vibrational motion could be toned down by about a factor of 100? I agree: it would be very educational to have an option where the displacements were properly scaled according to frequency: http://molecularmodelingbasics.blogspot.com/2010/06/geometry-and-molecular-motion.html > > (I was using a G09 output of hydrogen peroxide, run at M06/6-311++G**) > > On a second note, has there been thought to provide a database of > ground state molecules, with IR and NMR spectra for the smaller > entities? This would be valuable for the average user, who doesn't > have access to computational software and/or doesn't know how to use > computational software. > > So, my questions for everyone: > * is a molecular database a good idea? > * is it something that can be hosted on Avogadro.net? > * how should it be done? what format should be adopted? I believe this is within the scope of the Quixote project: http://quixote.wikispot.org/Front_Page > > Regarding the last: CML doesn't retain spectral data. It would be very > simple for me to provide a gaussian output file, *.g09, that can be > read by Avogadro. (FYI: DFT is great in that the vibrational > frequencies do not require correction (scaling factor is between 0.98 > and 1.02).) > > Your thoughts? > Dr. Roy Jensen > (==========)-----------------------------------------¤ > Chemistry, Grant MacEwan University > Room 5-172J, 10700-104 Avenue > Edmonton, AB T5J 4S2 > 780.633.3915 > > > ------------------------------------------------------------------------------ > Forrester recently released a report on the Return on Investment (ROI) of > Google Apps. They found a 300% ROI, 38%-56% cost savings, and break-even > within 7 months. Over 3 million businesses have gone Google with Google Apps: > an online email calendar, and document program that's accessible from your > browser. Read the Forrester report: http://p.sf.net/sfu/googleapps-sfnew > _______________________________________________ > Avogadro-Discuss mailing list > Avogadro-Discuss@... > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > ```
 [Avogadro-Discuss] Vibration animation and molecular database... From: Roy Jensen - 2010-12-22 04:28:31 ```A colleague asked if In knew of any software for animation of molecular vibration. (She has explained that she would be flapping her arms in class if I didn't know of any ... and I am seriously thinking about claiming ignorance and installing a camera.) That said, I noticed that the animate feature of Avogadro *wildly* exaggerates the vibrational motion. The lowest setting is actually about 10 times greater motion than in reality! The higher settings actually see the atom vibrate through the molecular geometry! Perhaps the vibrational motion could be toned down by about a factor of 100? (I was using a G09 output of hydrogen peroxide, run at M06/6-311++G**) On a second note, has there been thought to provide a database of ground state molecules, with IR and NMR spectra for the smaller entities? This would be valuable for the average user, who doesn't have access to computational software and/or doesn't know how to use computational software. So, my questions for everyone: * is a molecular database a good idea? * is it something that can be hosted on Avogadro.net? * how should it be done? what format should be adopted? Regarding the last: CML doesn't retain spectral data. It would be very simple for me to provide a gaussian output file, *.g09, that can be read by Avogadro. (FYI: DFT is great in that the vibrational frequencies do not require correction (scaling factor is between 0.98 and 1.02).) Your thoughts? Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan University Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 ```
 Re: [Avogadro-Discuss] z-Matrix editor From: - 2010-12-13 20:12:30 ```Hi Jan, >-----Original Message----- >From: Jan Wahl [mailto:janwahl@...] >Sent: Sun 12/12/2010 13:03 >Subject: [Avogadro-Discuss] z-Matrix editor >Hi community, >i'm using Avogadro for several month and now i need the z-matrix editor tool. But i cant find it in avogadro. Do i have to install it seperatly??? I don't think that Avogadro currently has a z-matrix editor, although I'm sure it won't be too long before one appears, as most of the machinery is already in the code base. In the meantime, the CCP1GUI: http://sourceforge.net/projects/ccp1gui/ does have a z-matrix editor that you could use. Both programs support a variety of different file formats, so it shouldn't be too difficult to pass data between the two. >by the way... im using Mac OSX 10.6. The CCP1GUI should run on OSX 10.6 Best wishes, Jens -- Scanned by iCritical. ```
 [Avogadro-Discuss] z-Matrix editor From: Jan Wahl - 2010-12-12 13:03:37 ```Hi community, i'm using Avogadro for several month and now i need the z-matrix editor tool. But i cant find it in avogadro. Do i have to install it seperatly??? by the way... im using Mac OSX 10.6. Thanks for your help Jan Wahl ( Universität Frankfurt /Main, Germany) ```
 [Avogadro-Discuss] difference in Avogadro and obabel conversions From: Prashanth Athri - 2010-12-07 12:59:48 Attachments: Message as HTML     try_frm_Avg.pdb     try_frm_OB.pdb     try_no_connect.pdb

Showing 9 results of 9