From chemistry-request@server.ccl.net Sun Jun 24 07:49:58 2001 Received: from gip.u-picardie.fr ([193.49.184.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5OBnw503969 for ; Sun, 24 Jun 2001 07:49:58 -0400 Received: from u-picardie.fr (iris.sa.u-picardie.fr [195.83.150.33]) by gip.u-picardie.fr (8.9.3/8.9.3) with ESMTP id NAA12842 for ; Sun, 24 Jun 2001 13:49:57 +0200 Sender: fyd@u-picardie.fr Message-ID: <3B365123.41AB2E86@u-picardie.fr> Date: Sun, 24 Jun 2001 13:44:19 -0700 From: Francois Dupradeau Organization: Faculte de Pharmacie X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: AmberFFC version 1.2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I am pleased to announce the release of AmberFFC version 1.2. In its original version, AmberFFC was designed to convert six AMBER force fields (Amber 91, Amber 91X, Amber 94, Amber 96, Amber 98 and Amber 99) freely available in the public domain (Kollman's group, http://www.amber.ucsf.edu), for use with the Molecular Simulations Inc. (MSI, renamed into Accelrys Inc., San Diego, http://www.accelrys.com/) Discover molecular mechanics modules. With its new release (version 1.2), AmberFFC also converts three GLYCAM force fields developed by Woods et al. (http://glycam.ccrc.uga.edu) for the MSI/Accelrys software. AmberFFC is free for the academic users after signing a license. See http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/AmberFFC.htm Best regards Francois -- F.-Y. Dupradeau http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm From chemistry-request@server.ccl.net Sat Jun 23 17:06:33 2001 Received: from web4905.mail.yahoo.com ([216.115.106.30]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5NL6X527684 for ; Sat, 23 Jun 2001 17:06:33 -0400 Message-ID: <20010623210633.17265.qmail@web4905.mail.yahoo.com> Received: from [66.81.26.40] by web4905.mail.yahoo.com; Sat, 23 Jun 2001 14:06:33 PDT Date: Sat, 23 Jun 2001 14:06:33 -0700 (PDT) From: Sengen Sun Subject: Re: CCL:phase/orbitals To: chemistry@ccl.net In-Reply-To: <1691512@rosencrantz.reed.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I must re-emphasize my points in a different way in order to make them clear. My perceptions on the micro world and mechansims of chemical reactions can not be confined inside those mathematical models such as SCF, HFT, LCAO, DFT. The variation techniques, perturbation approxmations, etc. are mathematical techniques but NOT the fundamental laws of physics, although the concepts of the fundamental laws are adopted in various ways in them. No body has ever prove to me that unique spaces don't exist in the reality. But they obviously don't in those mathematical treatments. In an extreme, when an electron is excited to unlimited far to reach an ionization state, two distinct spaces are generated. I am certaily curious to think what are the intermediate states. Whenever I give such an example, some people want to express their views based on those particular mathematical models. Please don't this time. We stand in different territories. The mathematical models are very valuable in helping us understand in A LIMITED WAY. They are often conceptual muddy. I would compare HFT to a dough, and DFT to a mud. When the dough is found in an extreme and the mud in the other, you mix up the dough and mud. The neutralized data are wanderful, but you also make a conceptually muddy world. It is not appropriate to judge everything in the physical reality based on the products of the variation theories. I certainly have a lot of conflicts in my minds as everybody does. Especially, I am trying to break the routine to think about the mechanism of electrocyclization reactions. I can not just simply follow others because of the conflicts that can not be resolved in my mind. Come back to the main subject of experimental exploration of unique spaces. I would say because of the controversals in everybody's mind, there is too much risks to deny others based on these controversal thinking. Rather, we should look at them by technical details. If I found 10 manuscripts to be junks, I would still be very patient to look at the NO 11. An important scientific breakthrough could be made in such a way that most people can not accept based on their routine thinking. We have to minimize the risk of suppressing the opposite opinions. That is all what I can say. Again thanks every body for responces or attentions to my postings. --- Alan Shusterman wrote: > Sengen, > > I think part of the problem is that you are > insisting on a definition > of "molecular orbital" that is close to, but not in > agreement with, the one > used by other scientists. > > Your definition, "I see them as > > 3-dimensional spaces to accommodate electrons > > according to the fundamental physical laws." is not > the commonly accepted > definition. On the other hand, your definition > includes "I see them as...". > This asserts a personal point-of-view, and this > implies each person should be > able to make a molecular orbital into whatever they > would like it to be. This > isn't fair (and it certainly does not provide a > useful answer to the scientist > who asked the original question in this thread). > > I will tell you how "I see" molecular orbitals. I > think I am giving a > description that is historically and scientifically > grounded. > > Molecular orbitals are mathematical solutions to > the Fock equations for > a given system. > > > This statement carries several implications: > > 1. MOs are the result of a particular mathematical > approach. They > originate with a "mathematical model" (you deny this > in your note). They do not > have an independent existence (which you assert). > > 2. The Fock equations do not have a unique > solution. One can insist on > "canonical molecular orbitals" (these diagonalize > the Fock matrix), but this is > not necessary. Even when one insists on canonical > MOs, there is no unique > solution if two or more orbitals are degenerate. > Linear combinations of the > degenerate orbitals are just as good solutions. > Since there are many ways to > write the MOs for a given system, it is nonsensical > to say that an MO > corresponds to what you call a "3 dimensional space > accommodating an electron". > Your statement implies a unique space and there are > no such spaces. > (Additionally, MOs do not define a "space" in the > usual sense; all MOs make use > of the same "space"; they just assign different > numerical values to the points > in this "space".) > > 3. MOs appear in a mathematical and conceptual > model that assumes > electrons do not correlate their motions, but > fundamental physical laws say > that electrons do correlate their motions. Once we > accept this fundamental law > molecular orbitals vanish. > > > One more argument: Scientific principles demand > that I accept theories > only if they explain observations. Quantum mechanics > succeeds on this basis. > Part of QM is the variation principle. One way to > describe this principle is: > any model that fails to give the lowest energy for > an electronic state is > necessarily incorrect. Molecular orbital models > NEVER give the lowest energy > for an electronic state. Therefore, these models are > always incorrect. > > > Frankly, I don't think you should pursue this > argument with the > Computational Chemistry List. You can try to keep > the argument going by > insisting on your own definition of molecular > orbitals, but you will find that > people stop responding once they realize that you > are unwilling to accept the > commonly accepted definition of molecular orbital > (you probably can attract a > certain amount of pedantic email like mine, > however). > > > -Alan __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/ From chemistry-request@server.ccl.net Sat Jun 23 22:54:46 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5O2sk530464 for ; Sat, 23 Jun 2001 22:54:46 -0400 Received: from eyou.com ([61.136.62.73]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id WAA27941 for ; Sat, 23 Jun 2001 22:54:41 -0400 (EDT) Received: (qmail 35268 invoked from network); 24 Jun 2001 10:54:39 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.1 with SMTP; 24 Jun 2001 10:54:39 +0800 Received: (qmail 65561 invoked by uid 65534); 24 Jun 2001 10:54:40 +0800 Date: 24 Jun 2001 10:54:40 +0800 Message-ID: <20010624105440.65560.qmail@eyou.com> From: "王明韬" To: CHEMISTRY@ccl.net Reply-To: "王明韬" Subject: help Dear all: can somebody give me some examples of molecular dynamic simulations? How can i exhaustively analyze the results? My e_mail:wqsm@eyou.com. Thanks! --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽