From chemistry-request@server.ccl.net Thu Oct 25 06:14:32 2001 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9PAEVB18130 for ; Thu, 25 Oct 2001 06:14:32 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with ESMTP id f9PAHNG03001 for ; Thu, 25 Oct 2001 12:17:24 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id MAA25876 for ; Thu, 25 Oct 2001 12:17:01 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3BD7E683.F4315021@lctn.uhp-nancy.fr> Date: Thu, 25 Oct 2001 12:16:35 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Group theory Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear collegues, I have a problem with group theory. When you consider two electrons in a two-fold degenerate level (let say (e^2) configuration for a transition metal in a tetrahedral surrounding (Td point group)) it is easy two find the multielectronic symmetry with the symmetric and antisymmetric direct products. There are 6 possible configurations for two electrons in 4 spinorbitals. The spin multiplicity is either 1 or 3. The direct product (E * E) reduce to A1 + A2 + E and it is not straightforward to assign the spin label, since one cannot have both spin multiplicities for all spatial symmetry (1-A1, 3-A1, 1-A2, 3-A2, 1-E and 3-E give 16 states!) However, with the symmetric and antisymmetric direct products is it very simple : symmetric direct product: (E * E)+ = A1 + E which leads to 1-A1 and 1-E singlet electronic states (antisymmetric spin function and symmetric space function). antisymmetric direct product: (E * E)- = A2 leading to 3-A2 triplet state (symmetric spin function and antisymmetric space function). Now my problem is : what about when you have three electrons in a three-fold degenerate level ? For example, (t2^3) configuration for Td point group. Thanks in advance. -- ...Xav WARNING! NEW E-MAIL ADDRESS ! (u-nancy changed to uhp-nancy) Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Thu Oct 25 08:34:20 2001 Received: from aloha.unl.edu ([129.93.36.9]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9PCYJB20531 for ; Thu, 25 Oct 2001 08:34:20 -0400 Received: from localhost by aloha.unl.edu (AIX 3.2/UCB 5.64/4.03) id AA11773; Thu, 25 Oct 2001 07:19:35 -0500 Date: Thu, 25 Oct 2001 07:19:35 -0500 (CDT) From: To: Xavier ASSFELD Cc: chemistry@ccl.net Subject: Re: CCL:Group theory In-Reply-To: <3BD7E683.F4315021@lctn.uhp-nancy.fr> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Prof Assfeld: I have two papers on this subject, J. Chem. Phys. _45_, 2304 (1966) and Intern. J. Quantum Chem. _8_, 267 (1974) looking at this problem from different viewpoints. The CRUNCH program suite, available for downloading at http://phy-ggallup.unl.edu/crunch has a module that makes calculations of this sort. Regards, On Thu, 25 Oct 2001, Xavier ASSFELD wrote: > Dear collegues, > > > I have a problem with group theory. > When you consider two electrons in a two-fold degenerate level > (let say (e^2) configuration for a transition metal in a tetrahedral > surrounding (Td point group)) it is easy two find the multielectronic > symmetry with the symmetric and antisymmetric direct products. > > There are 6 possible configurations for two electrons in 4 spinorbitals. > The spin multiplicity is either 1 or 3. > The direct product (E * E) reduce to A1 + A2 + E and it is not > straightforward > to assign the spin label, since one cannot have both spin multiplicities > for all spatial symmetry (1-A1, 3-A1, 1-A2, 3-A2, 1-E and 3-E give 16 > states!) > > However, with the symmetric and antisymmetric direct products is it very > simple : > > symmetric direct product: > (E * E)+ = A1 + E which leads to 1-A1 and 1-E singlet electronic states > (antisymmetric spin function and symmetric space function). > > antisymmetric direct product: > (E * E)- = A2 leading to 3-A2 triplet state (symmetric spin function and > antisymmetric space function). > > Now my problem is : what about when you have three electrons in a > three-fold > degenerate level ? > For example, (t2^3) configuration for Td point group. > > Thanks in advance. > > -- > > ...Xav > > WARNING! NEW E-MAIL ADDRESS ! > (u-nancy changed to uhp-nancy) > > Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr > Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 > Universite Henri Poincare (F) 33 3 83 91 25 30 > F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Gordon A. Gallup Dept. of Physics and Astronomy University of Nebraska-Lincoln Lincoln, NE 68588-0111 Voice: (402)435-6967,(402)472-1230 FAX: (402)472-2879 http://physics.unl.edu/~ggallup/gallup.html http://www.unl.edu/Dissatt/ From chemistry-request@server.ccl.net Thu Oct 25 11:22:52 2001 Received: from rudjer.irb.hr (graovac@[161.53.128.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9PFMpB23210 for ; Thu, 25 Oct 2001 11:22:51 -0400 Received: from localhost (graovac@localhost) by rudjer.irb.hr (8.10.0/8.10.0VS) with ESMTP id f9PFPBo12121; Thu, 25 Oct 2001 17:25:11 +0200 (MET DST) Date: Thu, 25 Oct 2001 17:25:10 +0200 (MET DST) From: Ante Graovac To: Andrew Horsfield cc: Computational Chemistry List , Atomic Scale Design Network Subject: Re: CCL:Call for announcements (fwd) In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleague, I hope our MCC 2002 meting should be of some interest to comp. physicists & comp. chemists, and please, find below the data on that meeting, with kind regards, sincerely, Ante Graovac, Director of the MCC 2002. ---------------------------------------------------------------------------- > o Title of meeting MATH/CHEM/COMP 2002, The 17th Dubrovnik International Course & Conference on the Interfaces among Mathematics, Chemistry & Computer Sciences > o Venue Inter-University Center, Dubrovnik, Croatia > o Date June 24-29, 2002 > o URL of web page giving full details of meeting http://mcc.irb.hr From chemistry-request@server.ccl.net Thu Oct 25 13:31:01 2001 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9PHV0B24892 for ; Thu, 25 Oct 2001 13:31:01 -0400 Received: from unibas.ch (filou.chemie.unibas.ch [131.152.112.19]) by igor.urz.unibas.ch (PMDF V6.0-24 #41480) with ESMTP id <0GLR007Q9VGHLY@igor.urz.unibas.ch> for chemistry@ccl.net; Thu, 25 Oct 2001 19:33:53 +0200 (MET DST) Date: Thu, 25 Oct 2001 19:32:57 +0200 From: Stanislav Ivan Subject: CIS calculation To: chemistry@ccl.net Message-id: <3BD84CC9.84459E3F@unibas.ch> MIME-version: 1.0 X-Mailer: Mozilla 4.75 [en] (WinNT; U) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-Accept-Language: en Dear CCL'ers I am doing some CIS calulations on aromatic diketones and ketenes using G98 and some of my calculations suddenly crashed with following message: **** Warning!!: The largest alpha MO coefficient is 0.23974133D+03 Semi-Direct transformation. ModeAB= 4 MOrb= 22 LenV= 12275249 LASXX= 14632552 LTotXX= 14632552 LenRXX= 29666813 LTotAB= 15034261 MaxLAS= 63456756 LenRXY= 0 NonZer= 44299365 LenScr= 78724297 LnRSAI= 63456756 LnScr1= 107460383 MaxDsk= -1 Total= 279308249 SrtSym= T ITran= 3 Is there anybody with similar experience or some idea how to solve this problem ? All advices are very appreciated. Thanks in advance. Stan -- Stanislav Ivan Institut für Organische Chemie St. Johanns Ring 19 4056 Basel Switzerland Tel.: (+41) (61) 267 11 44 E-mail: stanislav.ivan@unibas.ch From chemistry-request@server.ccl.net Thu Oct 25 01:30:29 2001 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9P5USB11148 for ; Thu, 25 Oct 2001 01:30:29 -0400 Received: from sunix.sunesis.com ([192.168.1.9]) by mercury.sunesis.com with Microsoft SMTPSVC(5.0.2195.2966); Wed, 24 Oct 2001 22:32:27 -0700 Date: Wed, 24 Oct 2001 22:33:09 -0700 (PDT) From: "Warren L. DeLano" cc: Demetrio Antonio da Silva Filho , CHEMISTRY@ccl.net Subject: Re: CCL:Animate sequence of coordinates from TINKER In-Reply-To: <3BD673F4.1078799E@imim.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN X-OriginalArrivalTime: 25 Oct 2001 05:32:27.0187 (UTC) FILETIME=[6EC0B030:01C15D16] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f9P5UUB11149 PyMOL can directly read and animate Tinker's XYZ files without conversion. While PyMOL provides most of the same capabilites of VMD in this area, PyMOL has a different feel and many other strengths. I recommend you try both programs and go with the one you're more comfortable with. http://www.pymol.org On Wed, 24 Oct 2001, Hugo G. de Teran wrote: > VMD (http://www.ks.uiuc.edu/Research/vmd/) uses Babel to convert a series of > xyz to a series of PDB files which VMD reads as an animation. > I never tried this option, but this is what the documentation of the program > says. > Hope it helps, > Hugo > > Demetrio Antonio da Silva Filho wrote: > > > Dear CCL'ers, > > > > I am using TINKER to perform some MD calculations and I would like > > to animate the viewing of sequence of coordinates snapshots from > > a dynamic trajectory. > > > > Does anybody knows a free software able to read the TINKER .xyz > > files and animate them ? > > > > Thanks in advance, > > > > Demetrio Filho > > > > -- > Hugo G. de Teran Castaņon > G. R. Informatica Biomedica > Institut Municipal d'Investigacio Medica - IMIM > C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN) > > Ph: +34 93 221 10 09 ext 2340 > Fax: Fax: +34 93 221 3237 > > http://www1.imim.es/modeling/ > > > From chemistry-request@server.ccl.net Thu Oct 25 01:02:28 2001 Received: from web14905.mail.yahoo.com ([216.136.225.57]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9P52SB10064 for ; Thu, 25 Oct 2001 01:02:28 -0400 Message-ID: <20011025050520.56234.qmail@web14905.mail.yahoo.com> Received: from [195.87.179.176] by web14905.mail.yahoo.com via HTTP; Wed, 24 Oct 2001 22:05:20 PDT Date: Wed, 24 Oct 2001 22:05:20 -0700 (PDT) From: Alimet Ozen Subject: Re: CCL:Animate sequence of coordinates from TINKER To: Demetrio Antonio da Silva Filho Cc: CHEMISTRY@ccl.net In-Reply-To: <5.1.0.14.0.20011023180348.00b2bc20@deimos.email.arizona.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Demetrio, I checked just to be sure and the program I mentioned in my previous e-mail(MOLDEN) is able to read .xyz files of TINKER and it also can create molecular structure animations from .xyz files. Is that what you want? I hope it helps.. Best Regards Alimet Ozen --- Demetrio Antonio da Silva Filho wrote: > Dear CCL'ers, > > I am using TINKER to perform some MD calculations > and I would like > to animate the viewing of sequence of coordinates > snapshots from > a dynamic trajectory. > > Does anybody knows a free software able to read the > TINKER .xyz > files and animate them ? > > Thanks in advance, > > Demetrio Filho > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | > Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ===== alimet@asma.cmpe.boun.edu.tr http://www.geocities.com/alchemistrial http://www.geocities.com/alimet __________________________________________________ Do You Yahoo!? Make a great connection at Yahoo! Personals. http://personals.yahoo.com From chemistry-request@server.ccl.net Thu Oct 25 18:27:26 2001 Received: from garaged.fis.unam.mx ([132.248.33.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9PMROB28998 for ; Thu, 25 Oct 2001 18:27:25 -0400 Received: from correo.fc.uaem.mx (garaged.fis.unam.mx [132.248.33.226]) by garaged.fis.unam.mx (8.11.6/8.11.6) with ESMTP id f9PMV6S09240 for ; Thu, 25 Oct 2001 16:31:07 -0600 Sender: max@localhost.localdomain Message-ID: <3BD892AA.ECDE748C@correo.fc.uaem.mx> Date: Thu, 25 Oct 2001 16:31:06 -0600 From: Max Valdez X-Mailer: Mozilla 4.78 [es] (X11; U; Linux 2.4.12-ac3 i686) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: NAMD analysis tools References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL'rs I'm a newbie to NAMD-VMD or anything related to molecular dynamics, reading the user guide I could not find any tool to analyse velocities, energies or anything else from the ouput files, since they are binary, i cannot find a way to translate them to a xmgr or gnuplot format to read them. Is there anything obious I'm not seeing? Whis tool do the NAMD users use ?. I'm interested on free programs. I'm learning gromacs too, and it does have that kind of tools, i think there must be something for NAMD Thanks in advance, I will sumarize if it worths for the newbies like me Max