From owner-chemistry@ccl.net Wed Apr 22 03:12:00 2009 From: "Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner#,#tugraz.at" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39132-090421123315-30282-lKNveFt+aXAj3qX5meW6pA*|*server.ccl.net> X-Original-From: "Dipl.-Ing. Thomas Mitterfellner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 21 Apr 2009 18:02:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner^^^tugraz.at] Hello! I've been searching through the web and through the archives but I couldn't find a decent solution for making a movie of a molecular vibration one gets from a frequency calculation with Gaussian or Turbomole. While Gaussview, Molden, Molekel and Jmol (no imaginary modes, as it seems!), are able to display the vibrations, there is no easy option to create, say an animated GIF (with transparency!), or an MPEG. How do you go about animating molecular vibrations for insertion into a presentation? I'd appreciate any help (preferably, but not limited to linux/OSS solutions)! Thank you, Thomas From owner-chemistry@ccl.net Wed Apr 22 05:17:01 2009 From: "Sten Nilsson Lill stenil ~ chem.gu.se" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39133-090422045925-21734-cbLXTd1yHGWmheX/nmW3rA::server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 22 Apr 2009 10:59:09 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil|*|chem.gu.se] Dear Thomas, Chemcraft has this feature and it works perfectly OK to use it in e.g. PowerPoint presentations. It reads Gaussian frequency calculations, but not Turbomole calculations as far as I know. Please look at http://www.chemcraftprog.com/ for the details. Hope it helps, Sten > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" > [thomas.mitterfellner^^^tugraz.at] > Hello! > > I've been searching through the web and through the archives but I > couldn't find a decent solution for making a movie of a molecular > vibration one gets from a frequency calculation with Gaussian or > Turbomole. While Gaussview, Molden, Molekel and Jmol (no imaginary > modes, as it seems!), are able to display the vibrations, there is no > easy option to create, say an animated GIF (with transparency!), or an > MPEG. > How do you go about animating molecular vibrations for insertion into a > presentation? I'd appreciate any help (preferably, but not limited to > linux/OSS solutions)! > > Thank you, > > Thomas> > > Ph. D. Sten Nilsson Lill Dep. of Chemistry University of Gothenburg Kemigĺrden 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2873 Fax: +46-31-772 3840 E-mail: stenil(~)chem.gu.se Alternative e-mail: stenil(~)physto.se From owner-chemistry@ccl.net Wed Apr 22 09:38:00 2009 From: "William F. Coleman wcoleman[-]wellesley.edu" To: CCL Subject: CCL: Making movies from molecular vibrations easily Message-Id: <-39134-090422080318-1823-GlsgmZP61MsfsHAvndXyEw[a]server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--1d106b34.1d1069a6.c614ab5e" Date: Wed, 22 Apr 2009 07:09:18 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman!A!wellesley.edu] This is a multi-part message in MIME format. ----=_--1d106b34.1d1069a6.c614ab5e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit You can make animated gif files directly in GaussView 4. When looking at the vibrations, select Save Movie instead of Start Animation. You will then be prompted for a file name and location. In the GaussView Preferences you can set the quality of the movie, which determines the number of frames that will be saved (and the size of the file). If you are using GaussView this is a painless way to do the movie. Another approach would be to use a screen capture tool such as Camtasia. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--1d106b34.1d1069a6.c614ab5e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
You can make animated gif files direc= tly in GaussView 4.  When looking at the vibrations, select Save Movie= instead of Start Animation.  You will then be prompted for a file nam= e and location.  In the GaussView Preferences you can set the quality = of the movie, which determines the number of frames that will be saved (and= the size of the file).  If you are using GaussView this is a painless way to do the movie.  Another approach would be to = use a screen capture tool such as Camtasia.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules

----=_--1d106b34.1d1069a6.c614ab5e-- From owner-chemistry@ccl.net Wed Apr 22 11:48:01 2009 From: "Danni Harris danni:_:simbiosys.ca" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39135-090422091200-9298-esAULNRVyQdt+/YZBEzV1Q%server.ccl.net> X-Original-From: "Danni Harris" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 22 Apr 2009 09:40:11 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: "Danni Harris" [danni###simbiosys.ca] Thomas---I don't know of an application for viewing QM output of e.g. reaction coordinate or vibration animation ----that will output a movie directly but there is an application GIFMERGE that will take an output of GIF's from any viewer (e.g. molden) and merge them into a GIF animation. I forget whether there is a transparency feature...but check this out: http://the-labs.com/GIFMerge/ Danni > > Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" > [thomas.mitterfellner^^^tugraz.at] > Hello! > > I've been searching through the web and through the archives but I > couldn't find a decent solution for making a movie of a molecular > vibration one gets from a frequency calculation with Gaussian or > Turbomole. While Gaussview, Molden, Molekel and Jmol (no imaginary > modes, as it seems!), are able to display the vibrations, there is no > easy option to create, say an animated GIF (with transparency!), or an > MPEG. > How do you go about animating molecular vibrations for insertion into a > presentation? I'd appreciate any help (preferably, but not limited to > linux/OSS solutions)! > > Thank you, > > Thomas> > -- Danni Harris, Ph.D. Scientific Sales and Support Executive Computational Chemistry Software Development SimBioSys 135 Queens Plate Dr.; Unit 520 Toronto, Ontario M9W V61, Canada Tel. Head-Office: 416-741-4263 Mobile: 650-799-6637 Fax: 416-741-5084 Web: http://www.simbiosys.ca From owner-chemistry@ccl.net Wed Apr 22 13:09:00 2009 From: "Jerome Kieffer jerome.Kieffer(~)terre-adelie.org" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39136-090422072712-30307-9RcC0W859CjylMy+pE63nw .. server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 22 Apr 2009 13:26:56 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer..terre-adelie.org] > I've been searching through the web and through the archives but I > couldn't find a decent solution for making a movie of a molecular > vibration one gets from a frequency calculation with Gaussian or > Turbomole. While Gaussview, Molden, Molekel and Jmol (no imaginary > modes, as it seems!), are able to display the vibrations, there is no > easy option to create, say an animated GIF (with transparency!), or an MP= EG. > How do you go about animating molecular vibrations for insertion into a > presentation? I'd appreciate any help (preferably, but not limited to > linux/OSS solutions)! Try Gabedit it exports png (even with transparency) from Gaussian Freq calculation, then use mencoder with something like : mencoder "mf://anim*.png" -mf type=3Dpng:fps=3D25 -ovc lavc -lavcopts \ vcodec=3Dmsmpeg4v2 -o film.avi HTH --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Wed Apr 22 13:44:00 2009 From: "=?iso-8859-2?Q?Marek_Mal=FD?= marek.maly-.-ujep.cz" To: CCL Subject: CCL: Forcefield parameters transformation - derivation ? Message-Id: <-39137-090422132449-2370-vS6wvg2lmmd8TdzBoFhOgw!^!server.ccl.net> X-Original-From: =?iso-8859-2?Q?Marek_Mal=FD?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=iso-8859-2 Date: Wed, 22 Apr 2009 19:26:53 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-2?Q?Marek_Mal=FD?= [marek.maly^_^ujep.cz] Dear Lukasz, thank you very much for your info and especially for that two articles ! Best, Marek Dne Tue, 21 Apr 2009 09:52:49 +0200 Lukasz Cwiklik cwiklik**gmail.com napsal/-a: > > Sent to CCL by: Lukasz Cwiklik [cwiklik|,|gmail.com] > 2009/4/20 Marek Malý marek.maly[#]ujep.cz : >> >> Sent to CCL by: =?iso-8859-2?Q?Marek_Mal=FD?= [marek.maly%ujep.cz] >> Dear Lukasz, >> >> thank you for your answer but unfortunately >> neither "native" Amber forcefields nor GAFF >> ff contain proper parameters for (bonds, angles, dihedrals) >> involving Si atoms :(( This is the true reason why I have posted >> here my question ... > Dear Marek, > Technically speaking, after the procedure described in the Antechamber > tutorial you will end up with *.frcmod file where the missing > parameters will be listed. If your atoms and bonds are not 'typical' > then everything except of charges will be missed. Then the funny part > starts. You can fill these gaps using some other force fields (if > available) and/or do it based on quantum chemical calculations. And of > course there are not strict rules on how to go from ab initio to the > force field moreover, unfortunately, people rarely describe it clearly > in the papers. General strategy is to fit Lenard-Jones and bonding > parameters in order to reproduce ab initio potential energy surfaces. > I have two practical examples, they are connected with my recent work > so they are not necessarily the most representative but can give you > some flavor: > 1) Description of a derivation of Lennard-Jones parameters: Al-Halabi et al., J. Phys. Chem. A 107 (2003) 10615. > 2) Derivation of bond and angle constants: Wong-ekkabut et al, Biophys > J. 93 (2007) 4225. > None of them was done for Amber, maybe other CCL-ers can provide > better examples. > > Best, > Lukasz > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/