From chemistry-request@ccl.net Sun Jul 27 15:48:09 2003 Received: from web20606.mail.yahoo.com (web20606.mail.yahoo.com [216.136.226.164]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6RJm947010145 for ; Sun, 27 Jul 2003 15:48:09 -0400 Message-ID: <20030727194809.45010.qmail~at~web20606.mail.yahoo.com> Received: from [64.169.232.184] by web20606.mail.yahoo.com via HTTP; Sun, 27 Jul 2003 12:48:09 PDT Date: Sun, 27 Jul 2003 12:48:09 -0700 (PDT) From: Sengen Sun Subject: CCL: Comments on Orbitals - a practical approach of a theoretical chemist To: chemistry~at~ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I have been very busy recently with many other things. But I do wish to respond to the message posted by Victor Geskin on June 4, 03 in this List (http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+04+001). In the first part of the message, a good picture was drawn about what theoretical papers SHOULD look like. I do not think there is anything that I cannot agree with in this part. In the second part, Victor made some very concise (at least to me) analyses about the essence of MOs. But in conclusion, he consciously avoided any direct reply to whether the orbitals are real or not . I would conclude something very different. Based on his analyses, I would have to state clearly: Orbitals are mathematically real, but not physically. You don t know what orbitals mean physically unless you convert them to the electron density presentation. There is no physical reality corresponding to the naked orbitals. As some other people have already clearly stated in many occasions, orbitals have no physical meaning and no physical existence. Does it matter to be ambiguous? Let us apply some simple logic here: If orbitals are physically meaningless, orbital interaction is meaningless, orbital control is meaningless, and orbital stabilization and destabilization are meaningless. These are magic phrases to me. Does any body in this world really understand the orbital control theories in chemistry? In a discussion board of the Preprint Server, I compared orbitals to ghosts of no physically reality. As ghosts are physically meaningless, their fight, their interaction, and their control are meaningless and are beyond understanding in science. Some body wrote me a personal e-mail and said that orbitals and ghosts are different because orbitals are scientifically useful but ghosts are not. Orbitals are very very useful, but should be used appropriately. I greatly admire the realistic scientific attitudes of many greatest scientists such as Gell-Mann, Feynman, Dewar If you don t understand, admit it. In his late stage of life, Dewar changed his mind, and clearly recognized the hypnotic effect of the orbital control theories in chemistry. Chemists goal to understand chemical reactions is to understand how the electrons are relocated from old bonds to form new bonds; and what the kinetic and thermodynamic reasons are for the electron relocations. We wish to understand resisting forces and driving forces as the kinetic factors for the electron relocations. If we don t have this knowledge, we don t understand chemical reactions. It is simple and clear! This very important knowledge has been muddled up for decades as a result of our misuse of the orbital concept. How do orbitals control here? And control what? There is nothing wrong with Victor Geskin s choice of avoiding any direct reply as soon as the orbital concept can be used correctly. But I am trying to emphasize the importance of being conceptually clear in the interpretation of our computational results. Our modern computational technologies have reached an astonishing level of high accuracy (thanks to the effort of computational chemists). Unfortunately, our words have been very muddy for decades in the interpretation of complex chemical reactions such as concerted cycloadditions, and have caused conceptual confusions in our textbooks and the literature. Again, the philosophical questions remain. What do EXPLANATION and UNDERSTANDING really mean in science? What does MECHANISM mean in chemistry? Can we say that chemical reactions are controlled by orbital overlap integrals mathematical operations or a human activity? I am far from being tired of this discussion, and wish to continue in any ways. __________________________________ Do you Yahoo!? Yahoo! SiteBuilder - Free, easy-to-use web site design software http://sitebuilder.yahoo.com From chemistry-request@ccl.net Sat Jul 26 14:53:18 2003 Received: from cpmd.org (cpmd.org [195.176.20.84]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6QIrH47005157 for ; Sat, 26 Jul 2003 14:53:17 -0400 Received: (from cur@localhost) by cpmd.org (AIX4.3/8.9.3p2/8.9.3) id UAA15294 for chemistry~at~ccl.net; Sat, 26 Jul 2003 20:53:15 +0200 From: Alessandro Curioni Message-Id: <200307261853.UAA15294~at~cpmd.org> Subject: !!!New CPMD update: CPMD 3.7.2 finally released!!! To: chemistry~at~ccl.net Date: Sat, 26 Jul 2003 20:53:15 +0200 (MDT) X-Mailer: ELM [version 2.5 PL6] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Friends, finally CPMD 3.7.2 is ready! I encourage you to download this new version that includes: -Bug fixes -Improved linear scaling optimizers - -Improved OpenMP parallelization -Surfaces and polymers not implying orthotombic supercells -Generalized LSD calculations -Faster MD with norm conserving pseudopotentials (improved fnonloc algorithm) Moreover, the cpmd-test suite and the manual have been updated (including new tests and the needed pseudos) and the manual too. CPMD is distributed for free for non-commercial purposes at www.cpmd.org. Happy computing ! The CPMD Team From chemistry-request@ccl.net Mon Jul 28 11:35:59 2003 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6SFZw47009003 for ; Mon, 28 Jul 2003 11:35:59 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.20) id 19hA2X-0005Rc-N8 for chemistry{at}ccl.net; Mon, 28 Jul 2003 17:35:57 +0200 Message-ID: <3F2542D6.40308{at}mpi-bpc.mpg.de> Date: Mon, 28 Jul 2003 17:35:50 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: Amber and Namd Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Report: -0.5/6.0 ---- Start SpamAssassin results -0.50 points, 6 required; * -0.5 -- User-Agent header indicates a non-spam MUA (Mozilla) ---- End of SpamAssassin results X-Spam-Level: / X-Virus-Scanned: (clean) by exiscan+sophie Dear CCLers, Does anyone have any experience with using both Amber and Namd for MD simulations. I would like to discuss a bit the Berendsen coupling scheme for Temperature in the 2 software packages. If somebody is aquented with this and has a bit of time could you give me a telephone number where I can call and also let me know a good time for calling...its hard to describe on the email Thank you very much in advance, Best regards, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru{at}mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Mon Jul 28 10:09:26 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6SE9Q47005917 for ; Mon, 28 Jul 2003 10:09:26 -0400 Received: from email.unb.ca (root{at}newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h6SE9MkY023264 for ; Mon, 28 Jul 2003 11:09:22 -0300 Received: from [131.202.130.26] (HELO webmail1) by email.unb.ca (CommuniGate Pro SMTP 4.0.6) with ESMTP id 14216561 for chemistry{at}ccl.net; Mon, 28 Jul 2003 11:09:21 -0300 X-WebMail-UserID: l72k6 Date: Mon, 28 Jul 2003 11:09:03 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Oxygen in AutoDock..... Message-ID: <3F27C3CA@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=1.1, required 5, FROM_HAS_MIXED_NUMS, SPAM_PHRASE_00_01) Hi All, I have a question about oxygen atoms in the receptor when docking with AutoDock. I recently read that Autodock only allows oxygen to be a hydrogen-bond acceptor if it is bonded to a carbon atom, and it is not considerd an H-bond acceptor when bonded to two hydrogens (as in water molecules considered as part of the receptor). The statement was in regards to Autodock 2.2, and I am presently using Autodock 3.05. I'm wondering if anyone knows if that is still true, and I therefore would need to include a new atom type to have water oxygens considered as H-bond acceptors. Any help on this issue is greatly appreciated. Thank you, Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: robert.flight{at}unb.ca ******************************** "People think it must be fun to be a super genius, but they don't realize how hard it is to put up with all the idiots in the world." -Calvin from Calvin & Hobbes From chemistry-request@ccl.net Mon Jul 28 04:38:59 2003 Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6S8cw47029720 for ; Mon, 28 Jul 2003 04:38:59 -0400 Received: from localhost (horn@localhost) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id KAA03699 for ; Mon, 28 Jul 2003 10:38:57 +0200 (MET DST) Date: Mon, 28 Jul 2003 10:38:57 +0200 (MET DST) From: Anselm Horn X-Sender: horn@as1200-1 To: chemistry{at}ccl.net Subject: Re: CCL:Gaussian checkpoint files In-Reply-To: <1059218688.3f22650005e6a{at}webmail.boun.edu.tr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, > I think you should use %no save keyword > this way the check point file freshly created will not be written on to the > previous one. > It should be written after the line stating the check point file unfortunately, this is not a good idea, because the NOSAVE keyword really is a NOKEEP, i.e. the specified files are not kept but rather deleted. The manual says that NOSAVE "causes Link 0 to delete scratch files at the end of a run". This means that after the first run from a number of jobs all referencing the same chk file with NOSAVE the precious chk file will be gone. I suggest writing a script that copies the chk files before the calculation, runs the Gaussian jobs interactively, and finally deletes the chk files, if you do not have the disk space for the complete set of chk files. Regards, Anselm From chemistry-request@ccl.net Mon Jul 28 14:30:55 2003 Received: from dep.chem.rug.nl (dep.chem.rug.nl [129.125.7.81]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6SIUs47015589 for ; Mon, 28 Jul 2003 14:30:54 -0400 Received: (from uucp@localhost) by dep.chem.rug.nl (8.9.3/8.9.3/Debian 8.9.3-21) id UAA29991 for chemistry.-at-.ccl.net; Mon, 28 Jul 2003 20:30:54 +0200 X-Authentication-Warning: dep.chem.rug.nl: uucp set sender to spoel.-at-.rugmd64.chem.rug.nl using -f Received: from rugmd64.chem.rug.nl by dep.chem.rug.nl (AvMailGate-2.0.1.7) id 29986-0ED58AC3; Mon, 28 Jul 2003 20:30:54 +0200 Received: from localhost (spoel@localhost) by rugmd64.chem.rug.nl (SGI-8.9.3/8.9.3) with ESMTP id UAA25648 for ; Mon, 28 Jul 2003 20:28:49 +0200 (MDT) Date: Mon, 28 Jul 2003 20:28:47 +0200 From: David van der Spoel To: chemistry.-at-.ccl.net Subject: Gaussian03 64bit on Xeon/Opteron Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.7; AVE: 6.20.0.1; VDF: 6.20.0.49; host: dep.chem.rug.nl) Hi, is there anyone out there that knows how to compile Gaussian03 with full 64 bit addressing on a Xeon or Opteron processor? I do have access to the new Portland compiler with Opteron support (but no Opteron yet...) Groeten, David. ________________________________________________________________________ Dr. Ir. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@ccl.net Mon Jul 28 19:25:22 2003 Received: from upstate.edu (gw4.upstate.edu [139.127.9.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6SNPM47021268 for >ccl.net>; Mon, 28 Jul 2003 19:25:22 -0400 Received: from HSCHOSP-MTA by upstate.edu with Novell_GroupWise; Mon, 28 Jul 2003 19:25:06 -0400 Message-Id: >upstate.edu> X-Mailer: Novell GroupWise Internet Agent 6.0.4 Beta Date: Mon, 28 Jul 2003 19:24:46 -0400 From: "Michael Chen" >upstate.edu> To: >ccl.net> Subject: IMAGE probelm, Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, everyone, Hope everything goes fine for you. I have one problem repeated so many times, which I had no clues what was going on. The warning was like: ***** LEVEL -4 WARNING FROM ***** ***** Too many image Hbond acceptors generated ****************************************** BOMLEV ( -6) IS NOT REACHED. WRNLEV IS 5 This happened after CHARMM called for READ IMAGE, and DYNAMICS where the image would be updated every 5 steps, and hydrogen bonds when necessary. My system was as big as the size of 30726 atoms. Would any foreruner please tell me how should I shoot this down? This warning kept popping up to the point where there would be a coredump. Could this be a memory space porblem? Thank you very much for your answer and your time. May you have a nice day. ***************************************************** Michael Chen Department of Biochemistry & Pharmacology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 USA *****************************************************