From owner-chemistry@ccl.net Thu Jun 21 09:03:00 2012 From: "oguz gurbulak gurbulakoguz!=!yahoo.com" To: CCL Subject: CCL: about ccl programs Message-Id: <-47116-120621062005-24830-1rivS2WCoojV8OKI6LgONA\a/server.ccl.net> X-Original-From: "oguz gurbulak" Date: Thu, 21 Jun 2012 06:20:04 -0400 Sent to CCL by: "oguz gurbulak" [gurbulakoguz_-_yahoo.com] Dear All, I study on molecular modelling and molecular dynamics simulation method. I examined www.ccl.net web site and wanted to ask you some questions about the programs in the link below. Im interested in some of these programs and I want to use them for my academic studies. http://www.ccl.net/ccl/qcpe/QCPE_removed/section12.html.shtml How can I get and use these programs ? Should I obtain a licence and pay the fee to use these programs ? or Are these programs free to nonprofit organizations for academic studies ? Could you please give me some information about this issue ? Thank you very much for your attention. Best regards. Oguz GURBULAK Ph.D. Student Ege University Faculty of Science Department of Physics Atomic and Molecular Physics From owner-chemistry@ccl.net Thu Jun 21 09:37:00 2012 From: "VITORGE Pierre 094605 Pierre.VITORGE^^^cea.fr" To: CCL Subject: CCL: Differences between NBO orbitals and molecular orbitals Message-Id: <-47117-120620123938-15161-LdzYUJFt10z+zWplyuHsJg_+_server.ccl.net> X-Original-From: VITORGE Pierre 094605 Content-Language: fr-FR Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 20 Jun 2012 16:39:29 +0000 MIME-Version: 1.0 Sent to CCL by: VITORGE Pierre 094605 [Pierre.VITORGE ~ cea.fr] Yes Elizabeth, a NBO is localized on two atoms -to represent their bond- or a single atom, all this corresponding to a Lewis structure, while a MO does not have this restriction: it can very well be localized on more than two atoms. Furthermore, the NBO software estimates errors originated in not taking into account delocalization or in missing a bound this is the Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis. -- Pierre Vitorge Directeur de recherche CEA CEA Saclay, DEN,DPC,SECR Laboratoire de Radiolyse et de la Matiere Organique, LRMO   Evry : Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE, UMR 8587, CEA, Univ Evry, CNRS, http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr _ ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr _ ccl.net] De la part de Jim Kress ccl_nospam:-:kressworks.com Envoyé : mercredi 20 juin 2012 14:43 À : VITORGE Pierre 094605 Objet : CCL: Differences between NBO orbitals and molecular orbitals Sent to CCL by: "Jim Kress" [ccl_nospam^-^kressworks.com] Read this: http://www.chem.wisc.edu/~nbo5/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com/./ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com/./ccl.net] On Behalf > Of Eli Lam elizabeth.shlam|*|gmail.com > Sent: Wednesday, June 20, 2012 3:48 AM > To: Kress, Jim > Subject: CCL: Differences between NBO orbitals and molecular orbitals > > > Sent to CCL by: "Eli Lam" [elizabeth.shlam+*+gmail.com] Dear CCLers, > > I would like to ask why is orbitals plotted using NBO analysis different > from > the molecular orbitals without using NBO? I have learnt that NBO will lead to > a more localized orbital distribution while MO is more delocalized. Yet, I'm > confused why the molecular orbitals output from NBO plots are much > different > > from molecular orbitals: the electron density localized on different > > atoms when > comparing the molecular orbitals from NBO output and the single point run. > Please advise! > > Thank you very much for your help! > Best regards, > EliTo > recover the email address of the author of the message, please change the > strange characters on the top line to the /./ sign. You can also look up the X- > Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jun 21 17:37:00 2012 From: "Jim Kress ccl_nospam#,#kressworks.com" To: CCL Subject: CCL: about ccl programs Message-Id: <-47118-120621125612-3467-QxTy9zUxWtebc9MxKc3/wA#,#server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Jun 2012 12:55:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam a kressworks.com] Start here: http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeli ng Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com(a)ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com(a)ccl.net] On Behalf > Of oguz gurbulak gurbulakoguz!=!yahoo.com > Sent: Thursday, June 21, 2012 6:20 AM > To: Kress, Jim > Subject: CCL: about ccl programs > > > Sent to CCL by: "oguz gurbulak" [gurbulakoguz_-_yahoo.com] Dear All, > > I study on molecular modelling and molecular dynamics simulation method. I > examined www.ccl.net web site and wanted to ask you some questions > about the programs in the link below. Im interested in some of these > programs and I want to use them for my academic studies. > > http://www.ccl.net/ccl/qcpe/QCPE_removed/section12.html.shtml > > How can I get and use these programs ? Should I obtain a licence and pay the > fee to use these programs ? or Are these programs free to nonprofit > organizations for academic studies ? Could you please give me some > information about this issue ? > > Thank you very much for your attention. > > Best regards. > > Oguz GURBULAK Ph.D. Student > Ege University Faculty of Science > Department of Physics > Atomic and Molecular PhysicsTo > recover the email address of the author of the message, please change the > strange characters on the top line to the (a) sign. You can also look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Thu Jun 21 18:12:00 2012 From: "Van Dam, Hubertus J HubertusJJ.vanDam a pnnl.gov" To: CCL Subject: CCL: about ccl programs Message-Id: <-47119-120621144639-19829-8y1/taWEwLu+kXS5+pwLug:-:server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 21 Jun 2012 11:46:29 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam*|*pnnl.gov] Hi Oguz, This is a complicated question. The list you point to contains wide variety of packages being covered by a number of different licenses. Some of the information is clearly way out of date as well (who is interested in a package that runs on an Intel 80386 these days). Some of the packages are most likely gone, and for some problems there are currently better alternatives than what is on that list. Nevertheless some of it might still be relevant. I guess that in order to provide a sensible response to your question some more information about what you want to do would be useful. That way information on the current state of particular packages can be provided. Best wishes, Huub -----Original Message----- > From: owner-chemistry+hubertus.vandam==pnnl.gov::ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov::ccl.net] On Behalf Of oguz gurbulak gurbulakoguz!=!yahoo.com Sent: Thursday, June 21, 2012 3:20 AM To: Van Dam, Hubertus J Subject: CCL: about ccl programs Sent to CCL by: "oguz gurbulak" [gurbulakoguz_-_yahoo.com] Dear All, I study on molecular modelling and molecular dynamics simulation method. I examined www.ccl.net web site and wanted to ask you some questions about the programs in the link below. Im interested in some of these programs and I want to use them for my academic studies. http://www.ccl.net/ccl/qcpe/QCPE_removed/section12.html.shtml How can I get and use these programs ? Should I obtain a licence and pay the fee to use these programs ? or Are these programs free to nonprofit organizations for academic studies ? Could you please give me some information about this issue ? Thank you very much for your attention. Best regards. Oguz GURBULAK Ph.D. Student Ege University Faculty of Science Department of Physics Atomic and Molecular Physicshttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt