From chemistry-request@ccl.net Mon Jul 12 09:46:07 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CEk5G4025464 for ; Mon, 12 Jul 2004 09:46:06 -0500 Received: by CELEBRIS04 with Internet Mail Service (5.5.2655.55) id ; Mon, 12 Jul 2004 11:50:08 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C57B7@CELEBRIS04> From: Ian Hovell To: "'chemistry'" Subject: CCL: choice of computer for G03 Date: Mon, 12 Jul 2004 11:49:58 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I'm looking for the ideal computer for running G03. I was wondering what people on the list, when buying a new computer dedicated to Gaussian03, would go fo? Would people go for cpu speed, cache memory, RAM or hard disk. Where would the emphasise be? And what OS would you opt for. I'm sure these questions have been asked for before so if any body can point me to a URL they know, okay. Thanks for your help and time. Ian From chemistry-request@ccl.net Mon Jul 12 09:49:26 2004 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CEnPG4025801 for ; Mon, 12 Jul 2004 09:49:25 -0500 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.12.6/8.12.8) with SMTP id i6CEtN5L059563 for ; Mon, 12 Jul 2004 07:55:24 -0700 (PDT) (envelope-from announce_at_schrodinger.com) From: Schrodinger Announcements To: CCL Subject: New release of Schrodinger software available Date: Mon, 12 Jul 2004 10:52:23 -0400 Message-ID: <0712104105223.0@SVETLA> MIME-Version: 1.0 Content-type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CEnQG4025805 Schrodinger is pleased to announce the latest versions of its drug discovery software. Among the most significant new features are the Induced Fit protocol for modeling flexible receptor docking, and a new sampling algorithm and scoring function in extra-precision (XP) Glide. The Induced Fit protocol uses Glide and Prime to predict ligand-receptor complexes for active ligands that do not dock well into existing rigid receptors. The predicted receptor models from Induced Fit reduce the occurrence of false negatives in virtual screening. The enhanced sampling and new scoring functions in XP Glide improve docking accuracy and database enrichment by further eliminating false positives. Enhancements in constraints and improved input structure checking are also introduced in Glide 3.0. The new release also contains general improvements and enhancements for all products. To learn more about Schrvdinger products, or to download the latest release, please visit www.schrodinger.com. From chemistry-request@ccl.net Mon Jul 12 07:00:30 2004 Received: from charlotte.lfc.edu (charlotte.lfc.edu [164.68.1.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CC0TUS016001 for ; Mon, 12 Jul 2004 07:00:29 -0500 Received: from charlotte.lfc.edu (localhost [127.0.0.1]) by charlotte.lfc.edu (iPlanet Messaging Server 5.2 HotFix 1.26 (built Mar 31 2004)) with ESMTP id <0I0Q00C5EMN34N^at^charlotte.lfc.edu> for chemistry^at^ccl.net; Mon, 12 Jul 2004 06:59:28 -0500 (CDT) Received: from [164.68.15.250] by charlotte.lfc.edu (mshttpd); Mon, 12 Jul 2004 06:59:27 -0500 Date: Mon, 12 Jul 2004 06:59:27 -0500 From: guntetz^at^charlotte.lfc.edu Subject: Adding a new atom type to G03 UFF Calculation? To: chemistry^at^ccl.net Message-id: <166e7d8.7d8166e^at^charlotte.lfc.edu> MIME-version: 1.0 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.26 (built Mar 31 2004) Content-type: text/plain; charset=us-ascii Content-language: en Content-transfer-encoding: 7BIT Content-disposition: inline X-Accept-Language: en Priority: normal X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello All, I am currently trying to build in two new atom types into the UFF force field in Gaussian 03', but am having a bit of difficulty. Has anyone attempted this before? If so, could you possibly give me some pointers on how to go about it. Test585.com is the only real clue that I have to work with right now, and it is just not cutting it. Thanks, Thomas Z. Gunter From chemistry-request@ccl.net Mon Jul 12 09:50:02 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CEo1G4025848 for ; Mon, 12 Jul 2004 09:50:01 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 2A97547EF3 for ; Mon, 12 Jul 2004 10:54:47 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03019-03 for ; Mon, 12 Jul 2004 10:54:41 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id B79FF47EEB for ; Mon, 12 Jul 2004 10:54:41 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 12 Jul 2004 10:54:41 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: Question on molecular structure and QM Date: Mon, 12 Jul 2004 10:54:40 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FDBB^at^srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Question on molecular structure and QM Thread-Index: AcRl7QzoiYP7vCtOS+uiANz4Pw0yKgCLrvKw From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 12 Jul 2004 14:54:41.0139 (UTC) FILETIME=[291F8430:01C46820] X-Spam-Status: No, hits=3.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CEo2G4025852 Wouldn't the isomers simply be different solutions to the same non-B-O Hamiltonian, just as the various states of a molecule are different solutions? (By "the various states" I mean the ones that within the B-O approx. are labeled vibrational, rotational, and electronic). --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request^at^ccl.net]On Behalf Of Eric Scerri Sent: Friday, July 09, 2004 3:00 AM To: ccl Subject: CCL:Question on molecular structure and QM The following is a somewhat general philosophical question. I would very much appreciate the comments of computational chemists. In the philosophy of chemistry literature much has been made of the fact that molecular structure cannot be strictly deduced from QM. I am referring to the work of Guy Wooley in the UK and Hans Primas at the ETH. The basis of this claim is that structure comes after applying the Born-Oppenheimer approximation to fix the nuclei. These authors claim that in this sense molecular structure has not been "reduced" to QM. They point to the fact that the Hamiltonians for two isomers of an organic compound, for example, are identical in the absence of the B-O approximation and they conclude that a strictly QM calculation cannot therefore distinguish between the two structures in question. I would be happy to pull some references together for anyone interested in studying the original articles. But I just wanted to hear some general reactions to such claims. -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri^at^chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY^at^ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jul 12 09:52:34 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CEqXG4026007 for ; Mon, 12 Jul 2004 09:52:33 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 60B7B47EF3 for ; Mon, 12 Jul 2004 10:57:22 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03343-10 for ; Mon, 12 Jul 2004 10:57:16 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id DAA5047EEB for ; Mon, 12 Jul 2004 10:57:16 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 12 Jul 2004 10:57:16 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: time-dependent and time-independent QM Date: Mon, 12 Jul 2004 10:57:16 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA000492E3CE)at(srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Question on molecular structure and QM Thread-Index: AcRl7QzoiYP7vCtOS+uiANz4Pw0yKgCLrvKwAAEeb5A= From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 12 Jul 2004 14:57:16.0936 (UTC) FILETIME=[85FC4080:01C46820] X-Spam-Status: No, hits=3.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CEqYG4026013 A possibly related question: there are two versions of the Hamiltonian, the time-dependent and the time-independent. The former represents the evolution of a dynamic system; the latter represents the steady states of the system, and is the Hamiltonian used in most quantum-chemistry problems. I've never really understood the relationship between the time-dependent and time-independent equations, especially since this is where all the "weirdness" of QM comes into play. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Shobe, David Sent: Monday, July 12, 2004 10:55 AM To: CCL computational chemistry list (E-mail) Subject: RE: Question on molecular structure and QM Wouldn't the isomers simply be different solutions to the same non-B-O Hamiltonian, just as the various states of a molecule are different solutions? (By "the various states" I mean the ones that within the B-O approx. are labeled vibrational, rotational, and electronic). --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On Behalf Of Eric Scerri Sent: Friday, July 09, 2004 3:00 AM To: ccl Subject: CCL:Question on molecular structure and QM The following is a somewhat general philosophical question. I would very much appreciate the comments of computational chemists. In the philosophy of chemistry literature much has been made of the fact that molecular structure cannot be strictly deduced from QM. I am referring to the work of Guy Wooley in the UK and Hans Primas at the ETH. The basis of this claim is that structure comes after applying the Born-Oppenheimer approximation to fix the nuclei. These authors claim that in this sense molecular structure has not been "reduced" to QM. They point to the fact that the Hamiltonians for two isomers of an organic compound, for example, are identical in the absence of the B-O approximation and they conclude that a strictly QM calculation cannot therefore distinguish between the two structures in question. I would be happy to pull some references together for anyone interested in studying the original articles. But I just wanted to hear some general reactions to such claims. -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri)at(chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY)at(ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow)at(nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Jul 12 13:19:53 2004 Received: from hermes.lfc.edu (hermes.lfc.edu [164.68.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CIJqG4010557 for ; Mon, 12 Jul 2004 13:19:52 -0500 Received: from cynic-23 ([164.68.51.31]) by hermes.lfc.edu (PMDF V6.2-X11 #40990) with ESMTP id <0I0R01I764J4VR*at*hermes.lfc.edu> for chemistry*at*ccl.net; Mon, 12 Jul 2004 13:25:54 -0500 (CDT) Date: Mon, 12 Jul 2004 13:17:45 -0500 From: "Thomas Z. Gunter" Subject: CCL:G03 new atom type for UFF question To: "chemistry*at*ccl.net" Message-id: Organization: Lake Forest College MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-15; format=flowed Content-transfer-encoding: 8bit User-Agent: Opera7.23/Win32 M2 build 3227 X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2,TO_ADDRESS_EQ_REAL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello All, I am currently trying to build in two new atom types into the UFF force field in Gaussian 03', but am having a bit of difficulty. Has anyone attempted this before? If so, could you possibly give me some pointers on how to go about it. Test585.com is the only real clue that I have to work with right now, and it is just not cutting it. Thanks, Thomas Z. Gunter -- Using M2, Opera's revolutionary e-mail client: http://www.opera.com/m2/ From chemistry-request@ccl.net Mon Jul 12 13:11:18 2004 Received: from cirse.extra.cea.fr (cirse.extra.cea.fr [132.166.172.102]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CIBGG4009846 for ; Mon, 12 Jul 2004 13:11:16 -0500 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.extra.cea.fr (8.12.10/CEAnet-Internet.3.0) with ESMTP id i6CIHFu7019891 for ; Mon, 12 Jul 2004 20:17:15 +0200 (MEST) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.14) with ESMTP id ; Mon, 12 Jul 2004 20:17:15 +0200 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by muguet.saclay.cea.fr (8.12.10/CEAnet-internes.3.0) with ESMTP id i6CIHFHL013235; Mon, 12 Jul 2004 20:17:15 +0200 (MEST) Received: from [132.166.18.220] (llb1220.saclay.cea.fr [132.166.18.220]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id i6CIHBv7018821 ; Mon, 12 Jul 2004 20:17:12 +0200 (MEST) In-Reply-To: <9DD56492790889439F731F5BD6DACA000492E3CE/at/srvkyem1.americas.sc-world.com> References: <9DD56492790889439F731F5BD6DACA000492E3CE/at/srvkyem1.americas.sc-world.com> Mime-Version: 1.0 (Apple Message framework v618) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: Cc: CCL computational chemistry list (E-mail) , scerri/at/chem.ucla.edu From: hinsen/at/cnrs-orleans.fr Subject: Re: CCL:time-dependent and time-independent QM Date: Mon, 12 Jul 2004 20:17:43 +0200 To: "Shobe, David" X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CIBIG4009852 On Jul 12, 2004, at 16:57, Shobe, David wrote: > A possibly related question: there are two versions of the > Hamiltonian, the time-dependent and the time-independent. The former > represents the evolution of a dynamic system; the latter represents > the steady states of the system, and is the Hamiltonian used in most > quantum-chemistry problems. I've never really understood the > relationship between the time-dependent and time-independent > equations, especially since this is where all the "weirdness" of QM > comes into play. The Hamiltonian is the same in the time-dependent and the time-independent Schroedinger equations. The time-dependent one is the starting point, it describes the time evolution of an arbitrary quantum state of a system. The time-independent equation results if one then asks which quantum states have no time evolution (other than a variable phase factor). The interest in these states is twofold: 1) They describe the stable states, which one is often interested in. 2) They contain all the time-dependent information as well, because the stable states (eigenstates of the Hamiltonian) are a basis of state space. For an arbitrary initial quantum state, calculate the projections on the stable states. Then multiply each projection with the (trivial) time-dependent phase factor and the corresponding stable state. Sum up everything, and you have the time evolution of the initial state. Because of 2), the time-independent equation can be considered a particular approach to solve the time-dependent equation. > Wouldn't the isomers simply be different solutions to the same non-B-O > Hamiltonian, just as the various states of a molecule are different > solutions? (By "the various states" I mean the ones that within the > B-O approx. are labeled vibrational, rotational, and electronic). Assuming that by "solution to a Hamiltonian" you mean its eigenstates, no, not in general, though often to a good approximation. This leads back to the original question by Eric Scerri. I am not familiar with the articles he refers to, but I don't see why the B-O approximation would be crucial. With or without B-O, quantum mechanics gives the probability distribution of the atomic configurations. One can then search for well-defined maxima and call them "molecular structures", but that is an additional interpretation step made for convenience of discussion only. I suppose that all chemists are aware that molecules are not static, the atoms move around all the time. So "molecular structure" is a concept introduced as a convenience, it cannot be deduced strictly from quantum mechanics. --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen/at/llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Mon Jul 12 15:09:47 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CK9kG4021894 for ; Mon, 12 Jul 2004 15:09:46 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 0743047F54; Mon, 12 Jul 2004 16:14:36 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 31124-06; Mon, 12 Jul 2004 16:14:30 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 386DC47F58; Mon, 12 Jul 2004 16:14:29 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 12 Jul 2004 16:14:29 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: CCL:time-dependent and time-independent QM Date: Mon, 12 Jul 2004 16:14:28 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FDBD^at^srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL:time-dependent and time-independent QM Thread-Index: AcRoPEyZn16D4VbVR8eMpKL6RTilrgABXQqw From: "Shobe, David" To: , "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 12 Jul 2004 20:14:29.0147 (UTC) FILETIME=[D6112EB0:01C4684C] X-Spam-Status: No, hits=3.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CK9lG4021901 Where does the part where measuring a property of the system "resets" the quantum state of the system come in? That's always been mysterious: how does the system "know" it's being measured? Does the uncertainty principle rest on an assumption that one cannot make a measurement w/o temporarily adding one or more other particles to the system? And can you really do that temporarily, or are you permanently enlarging the system when you add particles? Another problem I have with understanding the time dependent Schroedinger equation is that it's a differential equation, so you need initial/boundary conditions to solve it, right? But the postulates imply that you can't know all the initial conditions...or can the initial "psi-0" function incorporate both what's known about the initial state and what's unknown? --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: hinsen^at^cnrs-orleans.fr [mailto:hinsen^at^cnrs-orleans.fr] Sent: Monday, July 12, 2004 2:18 PM To: Shobe, David Cc: CCL computational chemistry list (E-mail); scerri^at^chem.ucla.edu Subject: Re: CCL:time-dependent and time-independent QM On Jul 12, 2004, at 16:57, Shobe, David wrote: > A possibly related question: there are two versions of the > Hamiltonian, the time-dependent and the time-independent. The former > represents the evolution of a dynamic system; the latter represents > the steady states of the system, and is the Hamiltonian used in most > quantum-chemistry problems. I've never really understood the > relationship between the time-dependent and time-independent > equations, especially since this is where all the "weirdness" of QM > comes into play. The Hamiltonian is the same in the time-dependent and the time-independent Schroedinger equations. The time-dependent one is the starting point, it describes the time evolution of an arbitrary quantum state of a system. The time-independent equation results if one then asks which quantum states have no time evolution (other than a variable phase factor). The interest in these states is twofold: 1) They describe the stable states, which one is often interested in. 2) They contain all the time-dependent information as well, because the stable states (eigenstates of the Hamiltonian) are a basis of state space. For an arbitrary initial quantum state, calculate the projections on the stable states. Then multiply each projection with the (trivial) time-dependent phase factor and the corresponding stable state. Sum up everything, and you have the time evolution of the initial state. Because of 2), the time-independent equation can be considered a particular approach to solve the time-dependent equation. > Wouldn't the isomers simply be different solutions to the same non-B-O > Hamiltonian, just as the various states of a molecule are different > solutions? (By "the various states" I mean the ones that within the > B-O approx. are labeled vibrational, rotational, and electronic). Assuming that by "solution to a Hamiltonian" you mean its eigenstates, no, not in general, though often to a good approximation. This leads back to the original question by Eric Scerri. I am not familiar with the articles he refers to, but I don't see why the B-O approximation would be crucial. With or without B-O, quantum mechanics gives the probability distribution of the atomic configurations. One can then search for well-defined maxima and call them "molecular structures", but that is an additional interpretation step made for convenience of discussion only. I suppose that all chemists are aware that molecules are not static, the atoms move around all the time. So "molecular structure" is a concept introduced as a convenience, it cannot be deduced strictly from quantum mechanics. --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen^at^llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Mon Jul 12 12:15:08 2004 Received: from walnut.cc.columbia.edu (walnut.cc.columbia.edu [128.59.59.124]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CHF7G4005079 for ; Mon, 12 Jul 2004 12:15:07 -0500 Received: from walnut.cc.columbia.edu (localhost [127.0.0.1]) by walnut.cc.columbia.edu (8.12.11/8.12.11) with ESMTP id i6CHL9D0019565 for ; Mon, 12 Jul 2004 13:21:09 -0400 (EDT) Received: from localhost (ak2048@localhost) by walnut.cc.columbia.edu (8.12.11/8.12.3/Submit) with ESMTP id i6CHL9OS019561 for ; Mon, 12 Jul 2004 13:21:09 -0400 (EDT) X-Authentication-Warning: walnut.cc.columbia.edu: ak2048 owned process doing -bs Date: Mon, 12 Jul 2004 13:21:09 -0400 (EDT) From: Anil Korkut Sender: ak2048/at/columbia.edu To: chemistry/at/ccl.net Subject: normal modes problem/CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=1.5 required=7.5 tests=FROM_ENDS_IN_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I am doing an NMA calculation for a protein with 3000 atoms using charmm simulation package. I minimized my structure to a gradient of 1e-6 with 2000 steps of sttepest descent followed by about 8000 steps of ABNR. I know that the first six normal modes should have zero frequency. However, I got no frequency values for the first two normal modes!!!! The translational and rotational modes start at mode 3 and the vibrational modes start at mode 9 instead of 7. The frequency values are VIBRAN> PRINT NORM MODE 1 THRU 16 DIPO NORMAL MODES 1********** 2********** 3 -0.01 4 -0.01 5 0.00 6 0.00 7 0.00 8 0.01 9 1.51 10 1.76 11 2.40 12 3.03 13 3.40 14 3.76 15 4.05 16 4.29 I have done the same calculation with a different force field (opls-ua) using TINKER and results were as expected (i.e. no blank modes, no negative eigenvalues) The nomal mode 7 from tinker has very similar freq. value to normal mode 9 > from charmm. I also used BPTI as a sample protein and the same problem exists. Does anyone have any idea what is going wrong here? I can post my script, if anyone is interested. Thanks ______________________________________________________________ Anil Korkut Dept of Biochemistry and Mol. Biophysics Columbia University, 630 West 168th St, BB204 New York, NY 10032 office ph (212) 305 1846 ______________________________________________________________ From chemistry-request@ccl.net Mon Jul 12 13:35:04 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CIZ2G4012154 for ; Mon, 12 Jul 2004 13:35:03 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i6CIf0no001382 for ; Mon, 12 Jul 2004 11:41:04 -0700 Received: from u.washington.edu (konga.chem.washington.edu [128.95.128.222]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i6CIf0uf027958 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Mon, 12 Jul 2004 11:41:00 -0700 Message-ID: <40F2DB20.7060208!at!u.washington.edu> Date: Mon, 12 Jul 2004 11:40:32 -0700 From: Carsten Detering User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry!at!ccl.net Subject: TS in solvent Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Thanks to all who replied to my previous question about the transition state problem. Using Noeigentest in the keyword section worked. I have two further questions now: After having successfully optimized my transition state in the gas phase, I would like to optimize it in solution. I used #B3LYP/6-31g* opt SCRF=(PCM,TS,Modredundant,solvent=chloroform,READ) nosymmetry test SCRF=PCM doesnt seem to allow a TS keyword though. Is there a way to optimize to a TS using the PCM model? What would the keyword section have to look like? My second question concerns the optimization of the same structure to one its minima, also in solution. I have used #B3LYP/6-31g* opt SCRF=(PCM,solvent=chloroform,READ) nosymmetry test with radii=uff and sphereonh=XX, but the calculation stops with ------ Using the following non-standard input for PCM: radii=uff sphereonh=39 End of line while reading PCM input. Error termination via Lnk1e in /software/gaussian/g03_B.4/g03/l301.exe at Mon Jul 12 19:56:48 2004. ------ I am using cartesian coordinates in the input section. Am I missing a parameter, or what is causing the calculation to stop? Thanks a lot in advance for any helpful suggestions, Carsten From chemistry-request@ccl.net Mon Jul 12 15:45:29 2004 Received: from postfix4-1.free.fr (postfix4-1.free.fr [213.228.0.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CKjSG4026376 for ; Mon, 12 Jul 2004 15:45:28 -0500 Received: from [213.228.30.23] (nas-cbv-6-213-228-30-23.dial.proxad.net [213.228.30.23]) by postfix4-1.free.fr (Postfix) with ESMTP id 771A415DF84; Mon, 12 Jul 2004 22:51:27 +0200 (CEST) In-Reply-To: <9DD56492790889439F731F5BD6DACA0047FDBD!at!srvkyem1.americas.sc-world.com> References: <9DD56492790889439F731F5BD6DACA0047FDBD!at!srvkyem1.americas.sc-world.com> Mime-Version: 1.0 (Apple Message framework v618) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: <5497CBCC-D445-11D8-B2C9-000A95AB5F10!at!cnrs-orleans.fr> Cc: CCL computational chemistry list (E-mail) From: hinsen!at!cnrs-orleans.fr Subject: Re: CCL:time-dependent and time-independent QM Date: Mon, 12 Jul 2004 22:52:04 +0200 To: "Shobe, David" X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6CKjTG4026385 On 12.07.2004, at 22:14, Shobe, David wrote: > Where does the part where measuring a property of the system "resets" > the quantum state of the system come in? That's always been > mysterious: That depends on who you ask, I think that discussion is still open-ended. The "collapse of the wave function" is part of the original Copenhagen interpretation of the meaning of the wave function. However, there are other interpretations. As the term "interpretation" implies, the choice of one does not change the maths - the equations and wave functions remain the same. The real problem in that discussion is that "measurement" needs to be defined. In a pure quantum world, there are particles interacting, all subject to the same laws, and the whole universe is governed by a single huge wave function. No measurements, no problems. Various definitions of measurements have been proposed, but none has yet been found to be without problems. Some say that measuring implies human consciousness - hence the paradox known as "Schrvdinger's cat". Others say that measurement is an interaction with a classical object, but that would imply that quantum mechanics needs to be defined in terms of its own limiting case, classical mechanics. > how does the system "know" it's being measured? Does the uncertainty > principle rest on an assumption that one cannot make a measurement w/o > temporarily adding one or more other particles to the system? And can > you The strict mathematical formulation of the uncertainty principle is in terms of wave functions, thus independent of any one interpretation. Many formulations in plain language depend on a choice of interpretation, however. > Another problem I have with understanding the time dependent > Schroedinger equation is that it's a differential equation, so you > need initial/boundary conditions to solve it, right? But the > postulates imply that you Yes, you need to know the initial quantum state. > can't know all the initial conditions...or can the initial "psi-0" > function incorporate both what's known about the initial state and > what's unknown? Right. That's again part of the interpretation problem. But not the worst in practice, as the question of time propagation of a given quantum state rarely occurs in real-life questions. That is perhaps another reason why the time-independent equation is so much more used in practice. ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen!at!llb.saclay.cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Mon Jul 12 11:38:12 2004 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6CGcBG4001580 for ; Mon, 12 Jul 2004 11:38:11 -0500 Received: (qmail 7828 invoked by uid 510); 12 Jul 2004 16:44:12 -0000 Received: from elewars(at)trentu.cA by mx3.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (f-prot: 4.4.1/3.14.11. spamassassin: 2.62. Clear:RC:1:. Processed in 0.024491 secs); 12 Jul 2004 16:44:12 -0000 X-Qmail-Scanner-Mail-From: elewars(at)trentu.cA via mx3.trentu.ca X-Qmail-Scanner: 1.20rc3 (Clear:RC:1:. Processed in 0.024491 secs) Received: from unknown (HELO trentu.cA) (209.42.102.47) by mx3.trentu.ca with SMTP; 12 Jul 2004 16:44:12 -0000 Message-ID: <40F2C0EE.8030008(at)trentu.cA> Date: Mon, 12 Jul 2004 12:48:46 -0400 From: Errol Lewars User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: CCL: summary conformers and rate(at)trentu.cA Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 2004 July 12 Here is the summary of the answers I got to the question below. Thanks very much to all who responded (I hope I haven't omitted anyone). Those interested in cases like s-cis-butadiene/s-trans-butadiene + a dienophile might wish to note #4 below, and E. Goldstein, B. Beno, and K. N. Houk, JACS, 1996, 118, 6036. ========= QUESTION 2004 July 8 The rate of formation of products Pa and Pb from quickly interconverting conformers Ca and Cb is treated with the the Curtin/Hammett and Winstein-Holness equations (the Curtin-Hammett principle, in particular, is well-known): J. I Seeman, Chem Rev, 1983, 83, 83; E. L. Eliel, "From Cologne to Chapel Hill", ACS, 1990, pp. 31-33. Question: has anyone a reference to a discussion of the case of rapidly interconverting conformers Ca and Cb, where Ca, although the minor conformer, is the only one that can react with X to form a product CaX, through transition state Ta; intuition aside, has someone explicitly addressed whether the _experimental_ activation E is measuring the Ta-Ca energy difference, or the Ta-Cb difference? Thanks. EL ----------- #1 Per-Ola Norrby Provided that the interconversion is fast relative to the final reaction, the free energy of activation should be relative to the ensemble energy (which is slightly lower than the lowest of Ca and Cb). The apparent activation energy is taken from an expression where you consider the total concentration of reactant. The sole effect of the pre-equilibrium is to make the effective concentration lower, with a concominant lowering of the rate which corresponds exactly to the free energy difference between the reacting conformer and the free energy of the ensemble. You can get the latter by assuming a virtual species corresponding to the total concentration of the reagent, and use the standard Boltzmann expression. The above wasn't perfectly clear (I haven't digested my coffee yet), but it should be correct. The math is available in the Ph.D. Thesis of Torben Rasmussen (Copenhagen 2001), and he took much of it from H Maskil, "The Physical Basis of Organic Chemistry", Oxford 1985. /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon(at)kemi.dtu.dk tel +45-45252123, fax +45-45933968 ========== #2 Andreas Klamt Errol, sorry for replying with a theoretical aspect: Do you really expect a unique answer? The answer will depend on the question, whether the exchange rate between Ca and Cb is larger or smaller than the reaction rate. In the first case you will observe Ta-Ca as activation energy, in the seond case Ca-Cb!!! because this step becomes rate determining. I am not sure whether you ever will observe Ta-Cb as activation energy. Andreas klamt(at)cosmologic.de ================= #3 Philip Hultin We have been dealing with a similar question, and have had some arguments with referees on this question. I don't know of any experimental demonstrations, but Seeman's paper does make the point very clearly that populations DO matter, at least in what he calls the "Case II Kinetics" scenario. The total rate is a population-weighted sum of the two individual rates, which implies that the individual activation barriers play a population-weighted role in the "apparent" activation barrier you would measure experimentally. Please, let me know of any comments you receive on this question. Dr. Philip G. Hultin Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin(at)cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ ================= #4 Jose Ignacio Garcia-Laureiro Dear Prof. Lewars, Indeed, there is a very common situation in which that happens, namely the s-cis/s-trans conformational equilibrium of open-chain dienes in Diels-Alder reactions. For instance, only the s-cis conformer (BDc) of butadiene is able to react, whereas the s-trans (BDt), the major conformer, is inactive towards the cycloaddition. In these conditions, the experimental activation barrier is measuring the TS-BDt energy difference, and this is because the same reasons operating in the Curtin-Hammett equation: the preequilibrium constant s-cis/s-trans appears in the kinetic equation as a multiplicative term, so that the apparent rate constant is in fact the product between the kcis (representing the TS-BDc activation barrier), and K (the conformational equilibrium constant, representing the s-trans - s-cis energy difference). I hope this can help you. Best regards. Josi I. Garcma ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Jose Ignacio Garcia-Laureiro, Investigador Cientmfico del CSIC Depto. Quimica Organica. Instituto de Ciencia de Materiales de Aragon Facultad de Ciencias (edificio D). Universidad de Zaragoza-CSIC c/ Pedro Cerbuna, 12. E-50009 Zaragoza (Spain) Phone: +34 976762271 e-mail: jig(at)unizar.es Fax: +34 976762077 http://wzar.unizar.es/acad/fac/cie/quiorg/catalisis/index.htm ============== From chemistry-request@ccl.net Mon Jul 12 18:37:23 2004 Received: from acomp.usf.edu (acomp.usf.edu [131.247.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6CNbLG4002859 for ; Mon, 12 Jul 2004 18:37:22 -0500 Received: from [131.247.209.78] (HELO WILL) by acomp.usf.edu (CommuniGate Pro SMTP 4.1.5) with ESMTP id 7919703 for chemistry*at*ccl.net; Mon, 12 Jul 2004 19:43:23 -0400 From: "will" To: Subject: autodock pdbq file Date: Mon, 12 Jul 2004 19:43:16 -0400 Message-ID: <000a01c4686a$0111eab0$4ed1f783@WILL> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_000B_01C46848.7A004AB0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_60_70,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C46848.7A004AB0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_000C_01C46848.7A0357F0" ------=_NextPart_001_000C_01C46848.7A0357F0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Thanks to a lot of help from those on this board, I've gotten over many hurdles I've encountered in trying to use autodock without any linux or modeling experience. It seems now that the only problem I have is with the 'finish work.' I've gotten all the data my PI requested of me, but now need to make some docked illustrations for some publications. All of my pdbq files used in the dockings however have a problem with connectivity. Once saved as a pdbq file, it gets pretty messy. I've attached a picture of FAD as an example. If someone could please help me in getting around this problem, I would greatly appreciate it. I also have downloaded opendx and compiled it on cygwin, but am unable to compile CTC chemistry extensions for some reason using the cygwin makefile provided. I get the following error: Make: *** [bin/addbonds] error 1 So, the only program I'll have to depicting my modeling is ViPEr that came with ADT package and what I can do with PMV. Anyone with useful 'networks' for ViPEr that care to share, it would be greatly appreciated. Also, is it possible to make a 'docking movie' with ADT/ViPEr? Thank you for your time Will ewlowe*at*helios.acomp.usf.edu university of south florida department of chemistry and biochemistry ------=_NextPart_001_000C_01C46848.7A0357F0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Thanks to a lot of help from those on this board, = I’ve gotten over many hurdles I’ve encountered in trying to use autodock without any linux or modeling experience. It = seems now that the only problem I have is with the ‘finish work.’ I’ve gotten all the data = my PI requested of me, but now need to make some docked illustrations for some publications. All of my = pdbq files used in the dockings however have a = problem with connectivity. Once saved = as a pdbq file, it gets pretty messy. I’ve attached a picture = of FAD as an example. If someone = could please help me in getting around this problem, I would greatly appreciate = it. I also have downloaded opendx and compiled it on cygwin, but am unable to compile CTC chemistry extensions for some reason using = the cygwin makefile = provided. I get the following = error:

Make: *** [bin/addbonds] = error 1

So, the only program I’ll have to depicting my modeling is ViPEr that came with ADT package = and what I can do with PMV. Anyone = with useful ‘networks’ for ViPEr that = care to share, it would be greatly appreciated. Also, is it possible to make a ‘docking movie’ with = ADT/ViPEr? = Thank you for your time

Will

ewlowe*at*helios.acomp.usf.edu

university of south = florida

department of chemistry and biochemistry