From chemistry-request@www.ccl.net Wed Mar 17 00:43:08 1999 Received: from mail1.javanet.com (mail1.javanet.com [205.219.162.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA01919 Wed, 17 Mar 1999 00:43:08 -0500 (EST) Received: from monaco (ct-hartford-us419.javanet.com [209.150.34.168]) by mail1.javanet.com (8.9.3/8.9.2) with SMTP id AAA11780 for ; Wed, 17 Mar 1999 00:43:07 -0500 (EST) Message-Id: <3.0.6.32.19990317004418.0091dcd0@mail.javanet.com> X-Sender: gusev@mail.javanet.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 17 Mar 1999 00:44:18 -0500 To: chemistry@www.ccl.net From: Vladimir Gusev Subject: Re: Comp-Chem-List In-Reply-To: <199704100713.DAA24164@www.ccl.net> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCL, I am collecting "Molecular Simulation Idioms", and would appreciate any suggestions in this regard. By idioms I call trivial problems, methods, which have fundamental importance for simulations, and can possibly be explained on fingertips. The core of corresponding codes should be fairly short, and could be run on a low-end computer, yet be a great illustration. These examples should be useful for both beginners and seasoned workers. Examples of two such idioms, Drunkard's Walk and Metropolis Walk, can be seen at http://javanet.com/~gusev/drunkard.html and http://javanet.com/~gusev/metropolis.html. At this time I am planning to add a third one to the list: umbrella sampling. I would also appreciate your opinion about the usefulness of such undertaking in principle. I will post a summary if there is interest. Vladimir gusev@javanet.com From chemistry-request@www.ccl.net Wed Mar 17 06:22:56 1999 Received: from nmr-v.ioc.ac.ru (root@nmr-v.ioc.ac.ru [193.233.3.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA04031 Wed, 17 Mar 1999 06:22:40 -0500 (EST) Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.8.7/8.8.7) with ESMTP id OAA06207 for ; Wed, 17 Mar 1999 14:35:45 +0300 Sender: val@nmr-v.ioc.ac.ru Message-ID: <36EF9391.882A6A1C@cacr.ioc.ac.ru> Date: Wed, 17 Mar 1999 14:35:45 +0300 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.30 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_post Subject: Re: CCL:ZINDO program-Summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, From the summary it is clear that there is no shareware or freeware ZINDO program available. I have some questions that are not directly related to the summary, however, it would be interesting to know what other CCL members think on these and what the answers may be. 1. Some points in the recent discussion confused me a little: ... > ZINDO is only available from MSI ... > ZINDO belongs to MSI ... > PM3tm is only found in Spartan. ... It sounds like The Methods are copyrighted and protected being used elsewhere. Unlikely possible a program (or a method) could become popular without any papers published in the literature and describing them in details. On the other hand, if the method and parametrization are known it means, in principle, anybody can write the program based on this information. Is it possible to publish something in the Open Literature and copyright it so, that incorporating the data into another programs will be forbidden ? 2. Reading the articles published some time ago (i.e. 7-15 years ago or so) one often finds the sentence like this: "...the program is available from authors upon request". On more recent publications this is rare case and, sometimes, even if it is - really it doesn't. Next, there are a lot of attempts to port programs, make GUI, create huge software packages from existing code (modern commercial products), etc. Does it mean that computational chemistry is over-saturated with different method/programs and nowadays the application rather than development is the main goal of theoretical chemists? 3. The Quantum Chemistry Program Exchange (QCPE) has been mentioned (only ones) in the discussion. It seems, however, this type of software distribution is not very popular now (correct me if I am wrong). Has QCPE influenced the progress of computational chemistry earlier? If so, what trends made this way of code development less effective now? any suggestions and discussion are welcome. best regards, Valentin. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@www.ccl.net Wed Mar 17 09:35:23 1999 Received: from icp.ac.ru (icp.ac.ru [193.233.43.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA10713 Wed, 17 Mar 1999 09:35:14 -0500 (EST) Received: from phot2.pc.icp.ac.ru (phot2.pc.icp.ac.ru [192.168.1.93]) by icp.ac.ru (8.9.1/8.9.1) with SMTP id RAA01105 for ; Wed, 17 Mar 1999 17:36:02 +0300 (MSK) Message-ID: <36F05813.B50@icp.ac.ru> Date: Wed, 17 Mar 1999 17:34:11 -0800 From: "Mikhayl F.Budyka" Reply-To: budyka@icp.ac.ru Organization: ICPR X-Mailer: Mozilla 3.0Gold (Win95; I; 16bit) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Excited states by DFT (B3LYP) Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, I would be grateful for any information about any program for the excited states calculations in the frame of DFT methods (especially by B3LYP). Thanks in advance, Mikhayl Budyka budyka@icp.ac.ru From chemistry-request@www.ccl.net Wed Mar 17 10:45:40 1999 Received: from pp2.shef.ac.uk (pp2.shef.ac.uk [143.167.1.32]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA11201 Wed, 17 Mar 1999 10:45:36 -0500 (EST) Received: from [143.167.103.254] (helo=ramsley.shef.ac.uk) by pp2.shef.ac.uk with esmtp (Exim 2.02 #5) id 10NIVB-00067A-00 for CHEMISTRY@www.ccl.net; Wed, 17 Mar 1999 15:45:01 +0000 Received: from RAMSLEY/MAILQUEUE by ramsley.shef.ac.uk (Mercury 1.44); 17 Mar 99 15:45:01 +0000 Received: from MAILQUEUE by RAMSLEY (Mercury 1.43); 17 Mar 99 15:44:55 +0000 From: "A.Schuffenhauer" To: CHEMISTRY@www.ccl.net Date: Wed, 17 Mar 1999 15:44:52 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:ZINDO program-Summary Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-ID: <6964761417D@ramsley.shef.ac.uk> > Date: Wed, 17 Mar 1999 14:35:45 +0300 > From: val > Organization: IOC > To: CCL_post > Subject: CCL:ZINDO program-Summary Dear CCL'ers val wrote: > It sounds like The Methods are copyrighted and protected being > used elsewhere. > Unlikely possible a program (or a method) could become popular > without any papers published in the literature and describing them > in details. On the other hand, if the method and parametrization > are known it means, in principle, anybody can write the program > based on this information. Yes, but there are examples, there exact desription of the method is not available in the open litaerature. For instance, in the user manual of Gaussian 94 are references (about the SCI-PCI method) contained , which were marked as "in preparation". Four years later, 1998, I tried to look them up, but according to a search in CAS-Online, these articles seemed never have been published. However, I do agree, that a method will not become really popular if they are not described in literature. > Next, there are a lot of attempts to port programs, make GUI, > create huge software packages from existing code (modern commercial > products), etc. > Does it mean that computational chemistry is over-saturated with > different method/programs and nowadays the application rather than > development is the main goal of theoretical chemists? Since is now possible to apply many of the methods, formerly restricted to rather small structure to larger molecules, which are not only of theoretical interest, you will find the users of programmes like Gaussian or the semiempiric methods not only among theoretical chemists. A PM3 optimisation of a small organic molecule may very be completed in a shorter time than required to generate the input file with an text editor only . I gave some PhD students in organic Chemistry, which were quite familiar with the normal office computer appilcations, but didn't have used any computaional chemistry software, tutorials in using mopac. Doing this I made made the experience, that the understanding of the structure of the input and result files is a non trivial and somehow off-putting problem for many chemists, who are in general interested in the methodes but don't have an longer experience in theoretical chemistry. The development of front ends easy to use and porting to hardware and/or operating systems plattforms, which are commonly used are important steps to make a method interesting for a wider range of users as a standard application. From a teaching point of view, an intuitive front end of programmes saves time in explaining the mere handling of the programme, which can be better used to explain the methodical background and the implications of it. And after all, what could be more rewarding for a method, as being accepted as a research tool by a wide range of users? Best regards Ansgar Dr. Ansgar Schuffenhauer Department of Informational Studies University of Sheffield Western Bank Sheffield S10 2TN E-mail: A.Schuffenhauer@Sheffield.ac.uk From chemistry-request@www.ccl.net Wed Mar 17 11:01:18 1999 Received: from mnvax.irfmn.mnegri.it (mnvax.irfmn.mnegri.it [195.61.203.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA11504 Wed, 17 Mar 1999 11:01:14 -0500 (EST) Message-Id: <199903171601.LAA11504@www.ccl.net> Received: from pcamb4.irfmn.mnegri.it by mnvax.irfmn.mnegri.it with SMTP; Wed, 17 Mar 1999 17:00:58 +0100 From: "pelagatti" To: "CCL_post" Subject: geometry minimization method Date: Wed, 17 Mar 1999 17:01:04 +0100 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL'ers I would like to know your opinion about the performances of geometry minimization methods (particularly the semi-empirical ones) in the cases of molecules containing various eteroatoms, such as organophosphorus. Is PM3 better than AM1 or NDO's ? In this case, does it depend on the molecule analyzed or is it a general rule ? I will summarize your kind answers. Thank you very much in advance Stefano Dr. Stefano Pelagatti Istituto di ricerche farmacologiche Mario Negri via Eritrea 62 Milan, Italy phone: +390239014499 E-Mail pelagatti@irfmn.mnegri.it From chemistry-request@www.ccl.net Wed Mar 17 13:38:07 1999 Received: from karplus0.harvard.edu (tammy.harvard.edu [128.103.92.198]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA24066 Wed, 17 Mar 1999 13:38:07 -0500 (EST) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by karplus0.harvard.edu (8.8.2/8.8.2) with ESMTP id NAA18288; Wed, 17 Mar 1999 13:51:28 -0500 (EST) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id NAA19247; Wed, 17 Mar 1999 13:26:40 -0500 (EST) Date: Wed, 17 Mar 1999 13:26:40 -0500 (EST) From: Qiang Cui To: "Mikhayl F.Budyka" cc: chemistry@www.ccl.net Subject: Re: CCL:Excited states by DFT (B3LYP) In-Reply-To: <36F05813.B50@icp.ac.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 17 Mar 1999, Mikhayl F.Budyka wrote: > Dear CCL'ers, > > I would be grateful for any information about any program for the > excited > states calculations in the frame of DFT methods (especially by B3LYP). Play with TD-DFT in Gaussian98. For reference, look for some work by Salahub or Alrich. > Thanks in advance, > > Mikhayl Budyka > budyka@icp.ac.ru > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: budyka@icp.ac.ru > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > ___________________________________________________________________________ Qiang Cui Dept. of Chem. _ __..-;''`--/'/ /.',-`-. Harvard Univ. (`/' ` | \ \ \\ / / / / .-'/`,_ 12 Oxford St., /'`\ \ | \ | \| // // / -.,/_,'-, Cambridge, MA 02138 /<7' ; \ \ | ; ||/ /| | \/ |`-/,/-.,_,/') (617)-495-8997 / _.-, `,-\,__| _-| / \ \/|_/ | '-/.;.\' (617)-495-1775 `-` f/ ; / __/ \__ `/ |__/ | Fax: (617)-496-3204 `-' | -| =|\_ \ |-' | http://yuri.harvard.edu/~qiang __/ /_..-' ` ),' // ((__.-'((___..-'' \__.' 805 Mt. Auburn Street Apt. 35 Watertown, MA 02472 (617)-926-6027 __________________________________________________________________________ From chemistry-request@www.ccl.net Wed Mar 17 14:37:06 1999 Received: from mx.seanet.com (dns2.seanet.com [199.181.164.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA26533 Wed, 17 Mar 1999 14:37:05 -0500 (EST) Received: from biggeek ([150.215.141.174]) by mx.seanet.com (8.8.8/Seanet-8.7.3) with SMTP id LAA09417; Wed, 17 Mar 1999 11:36:43 -0800 (PST) Message-ID: <001e01be70ad$7fa18ee0$ae8dd796@biggeek.wrq.com> From: "Mark Thompson" To: "val" , "CCL_post" Subject: Re: CCL:ZINDO program-Summary Date: Wed, 17 Mar 1999 11:36:43 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 There are non-commercial ZINDO implementations out there. Try ArgusLab http://www.seanet.com/~mthompson/ArgusLab/index.htm The program also supports AM1, MNDO, PM3, and Extended Huckel, and the self-consistent reaction field method. As for the literature, there is plenty of good literature on the ZINDO method. While there is no single paper that gives a comprehensive description of all the method's parameters, they are out there for those who wish to do some digging. As for PM3tm, try looking at the MNDO/d literature from Walter Thiel's group. -----Original Message----- From: val To: CCL_post Date: Wednesday, March 17, 1999 3:51 AM Subject: CCL:ZINDO program-Summary > > Dear CCL'ers, > >From the summary it is clear that there is no shareware or freeware >ZINDO program available. > >I have some questions that are not directly related to the summary, >however, it would be interesting to know what other CCL members >think on these and what the answers may be. > > >1. Some points in the recent discussion confused me a little: > > ... >> ZINDO is only available from MSI > ... >> ZINDO belongs to MSI > ... >> PM3tm is only found in Spartan. > ... > >It sounds like The Methods are copyrighted and protected being >used elsewhere. >Unlikely possible a program (or a method) could become popular >without any papers published in the literature and describing them >in details. On the other hand, if the method and parametrization >are known it means, in principle, anybody can write the program >based on this information. > >Is it possible to publish something in the Open Literature and >copyright it so, that incorporating the data into another programs >will be forbidden ? > > >2. Reading the articles published some time ago (i.e. 7-15 years >ago or so) one often finds the sentence like this: "...the program >is available from authors upon request". >On more recent publications this is rare case and, sometimes, >even if it is - really it doesn't. > >Next, there are a lot of attempts to port programs, make GUI, >create huge software packages from existing code (modern commercial >products), etc. >Does it mean that computational chemistry is over-saturated with >different method/programs and nowadays the application rather than >development is the main goal of theoretical chemists? > > > >3. The Quantum Chemistry Program Exchange (QCPE) has been mentioned >(only ones) in the discussion. It seems, however, this type of >software distribution is not very popular now (correct me if I am >wrong). > >Has QCPE influenced the progress of computational chemistry earlier? >If so, what trends made this way of code development less effective >now? > > >any suggestions and discussion are welcome. > > > best regards, > Valentin. > >==================================================================== > , , , , >Valentin P. Ananikov |\\\\ ////| /////| >NMR Group | \\\|/// | ///// | >ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | >Leninsky Prospect 47 | |===| | |===| | >Moscow 117913 | | | | | | | >Russia | | A | | | Z | | > \ | | / | | / >e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ >http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' > Fax +7 (095)1355328 Phone +7 (095)9383536 >==================================================================== > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: chemistry-request@www.ccl.net >-- Original Sender From: Address: val@cacr.ioc.ac.ru >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Wed Mar 17 17:35:28 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA07634 Wed, 17 Mar 1999 17:35:25 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id TAA06026 for ; Wed, 17 Mar 1999 19:32:09 -0300 (EST) Message-ID: <000e01be70c6$5b22dec0$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: NBO: $CHOOSE and $DEL Date: Wed, 17 Mar 1999 19:34:43 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear netters, In NBO 3..0 I generate a particular Lewis structure of an conjugated molecule, using $CHOOSE command, but I am not able to calculate the energy of deletion of some excited orbitals of this structure with $DEL. Is it possible? Thank you in advance, Sergio PS: I posted this question a week ago, with no answer... From chemistry-request@www.ccl.net Wed Mar 17 18:20:43 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA07866 Wed, 17 Mar 1999 18:20:43 -0500 (EST) Received: from oscdesk53.ccl.net (oscdesk53.ccl.net [192.148.249.53]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id SAA29599; Wed, 17 Mar 1999 18:20:43 -0500 (EST) Date: Wed, 17 Mar 1999 18:20:43 -0500 (EST) From: Gerald Lushington To: chemistry@www.ccl.net cc: gerald@ccl.net Subject: Workshop/Forum: Emerging Methods in Computational Chemistry and Materials Science Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII EMERGING METHODS IN COMPUTATIONAL CHEMISTRY AND MATERIALS SCIENCE Sheraton Four Points Hotel, Aberdeen MD April 29-30, 1999 The Army Research Laboratory Programming Environment and Training Program is pleased to announce a workshop/forum on Emerging Methods in Computational Chemistry and Materials Science. In this event, through a combination of seminar and forum environments, we hope to elucidate new developments in computational chemistry and materials science, explore their potential application to important DoD research, and help to promote DoD / academic cooperation and collaboration. The specific focus areas include: * Solvation Effects * Polymer Modeling * Materials and Surfaces ITINERARY: Solvation Effects (1:15 - 5:15 p.m., April 29) ----------------- * Dr. Daniel Chipman (University of Notre Dame) "Incorporation of Solvent Effects into Methods for Electronic Structure Calculation" * Dr. Jan Florian (University of Southern California) "The Structure, Reactivity, and Interactions of Small Organic Molecules in Aqeuous Solutions: A Computational Perspective" * Dr. Lawrence Pratt (Los Alamos National Laboratory) "Electronic Structure Calculations for Solution Species: the Quasi-Chemical Approximation of Statistical Thermodynamics" Polymer Modeling (8:30 a.m. - 12:15 p.m., April 30) ---------------- * Dr. Gregory Rutledge (Massachusetts Institute of Technology) "Applications of Molecular Modeling in Semicrystalline Polymers" * Dr. Shashi Karna (U.S. Air Force Research Laboratory) "New Developments in the Time-Dependent Hartree-Fock Theory and its Applications to Photonics Materials Development" * Dr. Peter Ludovice (Georgia Institute of Technology) "Simulation of Commercial Polymers with Intermediate Levels of Structural Order" Materials and Surfaces (1:30 - 5:15 p.m., April 30) ---------------------- * Dr. Emily Carter (UCLA) "First Principles Energetics, Kinetics, and Dynamics of Chemistry at Interfaces" * Dr. Susan Sinnott (University of Kentucky) "Computational Studies of Carbon Nanotubule-Based Probes, Membranes, and New Materials" * Dr. Jerry Whitten (North Carolina State University) "Future Directions of Theoretical Work in the Design of Materials and Surfaces" Please register online by April 23 at: http://www.arl.hpc.mil/PET/cta/ccm/workshops/emerg/reg.html For more information, please refer to the Workshop Web site at: http://www.arl.hpc.mil/PET/cta/ccm/workshops/emerg/index.html or contact: Margaret Hurley or Gerry Lushington hurley@arl.mil gerald@ccl.net 410-278-7591 614-292-6036