From ccl@www.ccl.net Thu Dec 4 08:39:09 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA02065; Thu, 4 Dec 1997 08:09:51 -0500 (EST) Received: from ns.base4.com for adit@extreme.chem.rpi.edu by bedrock.ccl.net (8.8.6/950822.1) id IAA18828; Thu, 4 Dec 1997 08:09:49 -0500 (EST) Received: from mail1.basefour.com (mail.base4.com [209.5.0.12]) by ns.base4.com (8.8.5/8.8.5) with ESMTP id IAA18848 for ; Thu, 4 Dec 1997 08:08:18 -0500 (EST) Received: from adi.basefour.com ([1.1.90.22]) by mail1.basefour.com (Netscape Messaging Server 3.01) with ESMTP id AAA19440 for ; Thu, 4 Dec 1997 08:09:48 -0500 Message-ID: <3486AB8D.81514CFD@extreme.chem.rpi.edu> Date: Thu, 04 Dec 1997 08:09:33 -0500 From: Adi Treasurywala Reply-To: adit@extreme.chem.rpi.edu Organization: Allelix Biopharm. X-Mailer: Mozilla 4.0 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Phosphate/sulfate bioisosterism. X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, Does anyon have any experience with the possible bioisosterism between the phosphate and the sulfate groups that they are willing/able to share? I seem to recall that somewhere this has been tried and it failed. Naturally I would be happy to summarize if there is sufficient response. Adi. -- ******************************** All views expressed here are only my own. Adi M Treasurywala Allelix Biopharma.Inc., 6850 Goreway Drive, Mississauga, Ontario. CANADA L4V 1V7. (905)677-0831 FAX (905)677-5344 em:adit@extreme.chem.rpi.edu ******************************** From jenninaj@mh.uk.sbphrd.com Thu Dec 4 09:39:11 1997 Received: from ns01.sbphrd.com for jenninaj@mh.uk.sbphrd.com by www.ccl.net (8.8.3/950822.1) id JAA02301; Thu, 4 Dec 1997 09:02:06 -0500 (EST) Received: by ns01.sbphrd.com; id JAA16369; Thu, 4 Dec 1997 09:02:07 -0500 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma016264; Thu, 4 Dec 97 09:01:47 -0500 Received: from hbu037.ha.uk.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA21414; Thu, 4 Dec 1997 09:01:46 -0500 Received: from hgu118.ha.uk.sbphrd.com (hgu118.ha.uk.sbphrd.com [139.136.157.118]) by hbu037.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/mh/970220) with ESMTP id OAA31725 for ; Thu, 4 Dec 1997 14:01:44 GMT Received: from localhost (jenninaj@localhost) by hgu118.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/clnt/970220) with SMTP id OAA08195 for ; Thu, 4 Dec 1997 14:01:43 GMT X-Authentication-Warning: hgu118.ha.uk.sbphrd.com: jenninaj owned process doing -bs Date: Thu, 4 Dec 1997 14:01:42 +0000 (GMT) From: Andy Jennings To: Comp-Chem-List Subject: Re.HyperChem: Incorrect geometries in amines..enough is enough Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks for all your comments over my erroneous statement that the nitrogen in phenylamine is planar. I have now got the message...in fact I have now got many messages...can we move onto something else? Cheers, Andy PS This e-mail does _NOT_require a number of replies. ================================================================= Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 ----------------------------------------------------------------- From ccl@www.ccl.net Thu Dec 4 11:43:44 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA03065; Thu, 4 Dec 1997 10:51:36 -0500 (EST) Received: from gatekeeper.es.dupont.com for fredvc@esalp1.dnet.dupont.com by bedrock.ccl.net (8.8.6/950822.1) id KAA25412; Thu, 4 Dec 1997 10:51:36 -0500 (EST) From: Received: from ns1.es.dupont.com (ns1.es.dupont.com [138.196.90.13]) by gatekeeper.es.dupont.com with SMTP id KAA06514 for ; Thu, 4 Dec 1997 10:51:36 -0500 Received: by ns1.es.dupont.com; id AA29724; Thu, 4 Dec 97 10:51:33 -0500 Message-Id: <9712041551.AA29724@ns1.es.dupont.com> Received: from esalp1.dnet; by esds01.dnet; Thu, 4 Dec 97 10:51:36 EST Date: Thu, 4 Dec 97 10:51:36 EST To: smtp%"info@microsimulations.com"@cdmhvx.dnet.dupont.com Cc: mail11:;@ccl.net (@dis:chem) Apparently-To: chemistry@ccl.net Subject: RE: CCL: 1000 MOST-CITED CHEMISTS RE: Armel, I took a quick look of the list and surprised to find that Allinger, NL is not on the list. I know that his paper on MM2/MM3 are widely cited. - - Lou Allinger IS on the list, # 374. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From charwel@chrs1.chem.lsu.edu Thu Dec 4 12:48:30 1997 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id LAA03298; Thu, 4 Dec 1997 11:40:36 -0500 (EST) Received: by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA26200; Thu, 4 Dec 1997 10:45:08 -0600 Date: Thu, 4 Dec 1997 10:45:07 -0600 (CST) From: Chris Harwell To: ccl Subject: SUMMARY of Beowulf for chemistry Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello, thanks very much to all who responded to my query about bewulf being used in chemsitry! Beowulf Systems in Computation Chemistry can also be found at: http://www.chem.lsu.edu/htdocs/people/crharwell/mybeo.htmlB These are in responce to a CCL and GU queries for information on beowulf systems in application to computational chemistry. We have been pondering the same thing, so if you get any feedback please let me know! I think that in terms of OS distributions it probably doesn't matter; what _is_ important is to get the interprocessor communications software from the Beowulf/Loki sites/home pages. GAMESS uses TCGMSG (if my failing memory) is correct, and so it will have to be reconciled with whatever is being used on Beowulf. ======================================================================= Craig W. Burkhart cburkhart@goodyear.com Goodyear Research ======================================================================= > Has anyone compiled and run gamess on a PC/Linux cluster? We've done this using FreeBSD ( FreeBSD ), as both Linux and BSD use the same tools and programming interfaces you should be able to do the same thing. > If so, with what amount of success? Very good, we started some years ago with 486 machines an now we're running on PPro 2000. > Any benchmarks or ballpark times? I'm CC: to nelson@iqm.unicamp.br. Dr. Nelson has the most recent results. > What hardware? (processor, motherboard, ethernet?/fast/myri/atm, mem) ASUSTEK MBoard with PPro200/256k cache, 64M RAM, NCR SCSI2 controller and Seagate HDs. We use PCI Fast Ethernet Cards based on DEC DE21140 chips or Intel Pro 10/100B these machines are attached to a Hub and to a Xylan switch. We have plans to move to faster network technologies in the next year. > What compiler? (gcc f2c or g77?) Both compiler produce good results, in true we're using a mix, some GAMESS's modules produce faster code with f2c others are faster under g77 (we're running 0.19/0.20) > What OS/distirbution? (linux/ redhat or debian?) We're runing this for the last 3 years or so, we started with freebsd 1.1.5 and now we're using 2.2.5. You should have no problems runing redhat/debian/slackware either. > Pedro Hello, I built a Linux cluster some time ago, you can get answers to most of your questions by having a look at our cluster's webpage:\ bigbrother I compiled GAMESS using g77 and it works fine. The problem with gamess is, it doesn't scale very well with the number of processors. When executing bench11.inp of the GAMESS test suite, I got a spedup of about 4, using 12-16 processors. This seems to be mainly because of GAMESS being only partially parallelized and also becaus of high latency times and low bandwith in our 100Mbps network. The distribution we installed was Slackware (Linux 2.0.25), but I would prefer Debian now. Oliver Kohlbacher (oliver@mpi-sb.mpg.de) Max-Planck-Institut fuer Informatik, Im Stadtwald, 66121 Saarbruecken Tel.: 0681-9325-505 Fax: 0681-9325-199 Hallo Chris, I don't know anything about this special cluster, and if you want to realize an cluster for parallel processing, then I have no experience. However, we have running a little test cluster for quantum chemical calculations also under Linux. We have running most of the known ab initio quantum chemical software packages including GAMESS (see also here ). The most important condition for good performance is an batch system; we are using the free available Generic NQS. The software file system is shared in the cluster via NFS. Up to date, there are no problems and we are using this machines also for production work. The most important limit in comparison to workstations is the main memory (we have 64 MByte on the PC's) and the memory cache. The performance is good for smaller jobs and goes back with jobs near the memory limit (see also the above mentioned web page, there are links to some benchmarks we have done with GAMESS under Linux, IBM RS6000 and Origin2000). Our hardware is Pentium PC (166 and 200) with 64 MB Memory, 4 GByte disk and Adaptec SCSI interface. We are using only the old BNC ethernet cable (without problems, but you should be sure to save the temporary integral files on a local disk and not via NFS). In the special case of GAMESS I have used the g77 compiler because of some error messages with f2c/gcc. Our Linux comes from a German distributor (SuSE GmbH), but I'm sure, that other distributions will work also. Hope this information will help ! Matthias Dr. Matthias Mann Computational Chemistry Group TU Dresden, Germany mann@coch03.chm.tu-dresden.de Chris, Iwould dearly love to hear of any responses you get to this question. I am trying to build such a system at th moment. First we are trying to build a prototype system (to see if we can do it) and then expand it (maybe). WHat we are looking at at the moment is (hopefully all free :-)); 486 DX2/66, PCI motherboard, 16MB, 500MB, 100Mbit ethernet. Then, if we can get this working at a reasonable speed, we might start to swap into updated hardware. Our first problem is to get free hardware, and work up from there, but if someone can show Gaussian / Gamess working, then it might be worth diving in at the deep-end. ALso, you might like to take a look at PAPERS as a connection medium (see papers for more info). ALso at that site is a discussion of the different networking methodologies that are best (ATM/ Ethernet/ PAPERS / whatever). Good luck, and please let me know how you get on. -- Simon Hogg, Imperial College, London, UK > > Are there any chemists out there who are using a beowulf cluster >of pcs type of system for computing? I haven't personally, but I know Morokuma's group at Emory does. A cluster of 14 Pentium Pro 200 PCs, I believe. Jaime Martell, Ph.D. P.O. Box 2317 Camille and Henry Dreyfus Fellow Batesville, AR 72503-2317 Biology and Chemistry Division Phone: 870-698-4688 Lyon College Fax: 870-698-4622 >I compiled GAMESS using g77 and it works fine. The problem with gamess is, >it doesn't scale very well with the number of processors. >When executing bench11.inp of the GAMESS test suite, I got a spedup of about >4, using 12-16 processors. This seems to be mainly because of GAMESS being >only partially parallelized and also becaus of high latency times and low >bandwith in our 100Mbps network. 1. Here at Ameslab, Scalable Computing Lab ameslab found that they had trouble getting faster than 1Mbps on Switched fast ethernet under linux for some packet sizes. Linux's tcp/ip stack and network drivers were really bad. Downloading the latest drivers for you ethernet card, and the latest version of linux might help. Performance was packet size dependent. For one code, you could increase the size of the problem, and thus the packet size, and have it finish much faster. 2. Bench11.inp is not big at all. You would never run such a job in parallel. Small parallel jobs sometimes take longer on multiple nodes, just because of all the "I'm done, are you done" talking. It only takes 18.6 CPU minutes (28 minutes Wall) on one of our 266MHz Alpha's. 3. CI is not the most scalable part of the code either. Kurt Glaesemann 201 Spedding Hall Ames Lab/Iowa State University Ames, IA 50011 ________________________________ Yes. Check out lobos . ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 BETHESDA, MD 20892-4255 USA Fax: (301) 496-5839 web Laboratory of Medicinal Chemistry, National Cancer Institute, & Lab. of Structural Biology, Div. of Computer Research and Technology ------------------------------------------------------------------------ Dear Chris, we are indeed thinking about building a beowulf cluster (like many other groups I guess). In particular we are considering a 16 Pentium Pro 200 machine, connected by means of a fast ethernet switch. >From the point of view of the hardware we are still evaluating the feasibility of our project. We are testing MPI on a 3 Pentium 166 MMX, ethernet connected system. Obviously, we will not obtain significant informations about performance from that system, but I must say that everything work nicely! (btw we used the RedHat 4.1 or 4.2 linux distributions) About the software. We developed a modified version of Gaussian94 that uses MPI as message passing library. It also use ScaLAPACK's parallel linear algebra routines for diagonalization and matrix multiplication. We developed that code on the Cray-T3E MPP system where we obtained good results (I can send you some data if you want). We ported the basic MPI inteface on our toy-PC-cluster and it works, but we do not yet know the actual performance of the ScaLAPACK library routines within G94. To use ScaLAPACK you have to scatter/gather the relevant matrices from/to the master and the workers processes and this imply a lot of communication overhead. If it's true that communications are **VERY** fast on the Cray-T3E, we are not so sure about the actual performance of MPI-based communications in a PCs cluster! We are very interested in testing our Gaussian94-MPI-ScaLAPACK code on a true [ already existing :-) ] Beowulf system, so I will be glad if you could copy me all the answers you obtain from the CCL (or I'll wait for a summary!) ---------------------------------------------------------------------- | SCALMANI Giovanni giovanni@sg2.csrsrc.mi.cnr.it ^^^ | Ph.D. Student o o | Dipartimento di Chimica Fisica ed Elettrochimica | | Universita' degli Studi di Milano \_/ | via C.Golgi, 19 Phone: ++39-2-26603254 | 20133 Milano (Italy) Fax : ++39-2-70638129 ---------------------------------------------------------------------- Hi, > Are you aware of anyone one using wien in parrallel on pc clusters? No. > If so do you know of any benchmarking/ performace testing ie how > parallelizable is wien? If you do k-point parallelization (WIEN97) it should run with full speed of each processor. Of course it depends on the cases you want to investigate if you have enough k-points to distribute. > > Any suggestions on > hardware configuration(proc, motherboard,mem, hardisk, fastether/atm/giga?) > software (compilers gcc vs g77?, message passsing,load balancing) > or os distribution (redhat or debian)? We use a SUSE distribution and g77 on a PII-266MHz. It has the speed of about 1/3-1/4 of a state-of-the-art SGI R10000, DEC Alpha-500MHz or IBM 120MHz processor. (The new HP or IBM 375-160MHz will be even faster). With k-point parallization you need just standard ethernet and a common NFS filesystem, no extra hardware, message passign software,... However, you need "full" memory on each node (probably at least 128 Mb, maybe even 512, depending on your needs). -------------------------------------------------------------------------- Peter BLAHA, Inst.f.Techn.Elektrochemie, TU Vienna, A-1060 Vienna Phone: +43-1-58801-5187 FAX: +43-1-5868937 Email: pblaha@email.tuwien.ac.at WWW: web -------------------------------------------------------------------------- > Are there any chemists out there who are using a beowulf cluster > of pcs type of system for computing? We have constructed an 80 processor Beowulf-class supercomputer called LoBoS (Lots of Boxes on Shelves). LoBoS will be scaled up to 136 processors next week. LoBoS' home page is: lobos and contains a more complete description of the equipment. We are in the process of adding benchmarks for different parallel topologies. BTW, the hardware pulse and queue management code seen on the web page are freely available. As a government lab we can't put much vendor-specific info on the web site (but we can talk about it). It is safe to say that, for our applications (QM and classical simulation) we are getting 10 times the price performance of the local supercomputer ! > Has anyone used gamess, gaussian, or Wien FLAPW on such a system? The test and current (Phase 2) systems have been in production use since April performing CHARMM, GAMESS and AMBER runs. >What hardware choices did you make (processor. motherboard etc.) ? We tested the DEC Alpha, PowerPC, Pentium Pro and PentiumII processors. The best price/performance was clearly (by a factor of 2-10) the Pentium Pro. The DEC Alpha remains an excellent processor so we are continuing to develop a 5 processor DEC Alpha cluster. Once we settled on the PentiumPro we tested 5 motherboards and found a small variance (+/- 5%) for well designed motherboards. Cheap motherboards which were/are available use the older Intel chipset and are 20-30% slower. > What compiler did you use (gcc,f2c, g77)? We tested 3 commercial compilers as well as f2c/gcc and g77. We are using the compiler from AbSoft. > What OS/Distribution did you use (linux/ redhat or debian?) All nodes use Linux. I think its safe to say that the Beowulf community is moving towards the use of RPM (RedHat) for installs and ensemble management software distribution, but we have been using Debian with good success. > Any suggestions to someone considering building such a system? 1. At a recent conference there was a general consensus that the hardware for up to 16 nodes was a "solved problem" when optimizing price performance. The equipment includes PentiumPros, a single Fast Ethernet NIC and a 16-port Fast Ethernet Switch (not hub). Add disk to suit your taste. 2. Since it sounds like you're doing QM work, you might consider the Dual PentiumPro configurations. You can amortize the cost of supporting hardware (disk, power supply, case etc) over two processors and improve your overall price/performance. 3. Don't be taken in by the Intel Bunny people and automatically buy a PentiumII. The PentiumII is a PentiumPro with MMX (useless for floating point ops) and faster memory access. Unfortunately, the advantages are offset by an off-chip cache that runs at half the speed of the PentiumPro. Our benchmarks showed that the PentiumII performance improvements barely scale up with the faster clock rates. Eric Billings Molecular Graphics and Simulation Laboratory National Institutes of Health >... >3. Don't be taken in by the Intel Bunny people and automatically buy a >PentiumII. The PentiumII is a PentiumPro with MMX (useless for >floating point ops) and faster memory access. Unfortunately, the >advantages are offset by an off-chip cache that runs at half the speed >of the PentiumPro. Our benchmarks showed that the PentiumII performance >improvements barely scale up with the faster clock rates. Another issue is the cost of processor in the future: PPro's architecture (on-chip cache) makes it very costly in production. This is another reason Intel came up with PentiumII with off-chip cache. The off-chip cache structure is also cheaper to expand, both in terms of size and clock speed. So bottom line is that PPro with on-chip cache has a better architecture than Pentium II for computional extensive work, but Intel might not lower the price further or devepop it more (high clock speed or more cache). The cost/performance ration of two CPU would change in the future. Xinjun C Xinjun J. Hou (hou@agouron.com) Agouron Pharmaceuticals, Inc. From ccl@www.ccl.net Thu Dec 4 13:43:02 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA03898; Thu, 4 Dec 1997 12:43:57 -0500 (EST) Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by bedrock.ccl.net (8.8.6/950822.1) id MAA00261; Thu, 4 Dec 1997 12:43:55 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id MAA38210; Thu, 4 Dec 1997 12:42:40 -0500 Sender: richard@TC.Cornell.EDU Message-ID: <3486EB8F.1372@tc.cornell.edu> Date: Thu, 04 Dec 1997 12:42:39 -0500 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Pieter Stouten CC: chemistry@ccl.net Subject: Re: CCL:HyperChem: Incorrect geometries in amines References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > There actually is at least one forcefield (MSI's CFF96) that is used in > Molecular Mechancis that does have properly puckered nitrogens. Are there > any other forcefields people know of, that do describe aniline etc. > properly? > > Thanks, > > Pieter Stouten My unofficial implementation of MMFF94 does seem to minimize to an out-of-plane result. Looking at Halgren's papers, I do see that "aniline, N puckered" is listed in the core parameterization (Table I, paper I). Richard Gillilan Cornell Theory Center richard@tc.cornell.edu From mclark@smtpgwy.isinet.com Thu Dec 4 15:41:57 1997 Received: from isinet.com for mclark@smtpgwy.isinet.com by www.ccl.net (8.8.3/950822.1) id OAA04759; Thu, 4 Dec 1997 14:41:26 -0500 (EST) From: Received: from smtpgwy.isinet.com ([198.62.99.211]) by pandora.isinet.com with SMTP id <14345>; Thu, 4 Dec 1997 14:42:53 -0500 Received: from ccMail by smtpgwy.isinet.com (SMTPLINK V2.11.01) id AA881275361; Thu, 04 Dec 97 14:37:15 EST Date: Thu, 4 Dec 1997 14:37:15 -0500 Message-Id: <9711048812.AA881275361@smtpgwy.isinet.com> To: "Dr. J. Phillip Bowen" Cc: chemistry@www.ccl.net, Pendlebury@isinet.com, _David_at_ISI__PHL@smtpgwy.isinet.com Subject: Re: CCL:G:Lists and Noble Prizes Dr. Allinger is on the list of the 1000 most cited chemists! he is the 374th most cited chemist on that list: Author name average total total rank cites articles cites ALLINGER NL 26.06 138 3596 374 Unfortunately, the MM2 and MM3 works may be cited hundreds of time, but not attributed to Allinger. There are 278 entries for direct citations of the programs mm2, mmp2, and mm3, without citing Allinger. Here are a few of them: Hits Cited Author Cited Work Volume Page Year 1 MM2 77 QCPE 395 1 MM2 85 1985 1 MM2 85 QCPE 1 MM2 MMP2 QCPE 395 1 MM2 MMPM PROGRAMS 1989 1 MM2 MOL MECHANICS 2 1 MM2 PROGRAM CHEM 3D 151 1990 1 MM2 PROGRAM MANUAL 1980 1 MM2 PROGRAM VERSION 1987 If each of these was only cited once, that would make his citation count at least 3874, moving him up about 50 positions, I didn't check the complete list, but many of the "cited works" are cited many times. Lots of articles just say they used MM2/3 without citing it. Unfortunately, there is no standard way that authors are citing software packages and versions that allows searching for them in a convenient way. There are several other scientists on that list whose citation counts would increase if citations of their software packages or other commercialized works were included. Also note that our citation counts do include the articles where Dr. Allinger is not the primary author. Dr. Matthew Clark Institute for Scientific Information http://www.isinet.com From SALVATORE.PROFETA.JR@monsanto.com Thu Dec 4 15:42:15 1997 Received: from gatekeeper3.monsanto.com for SALVATORE.PROFETA.JR@monsanto.com by www.ccl.net (8.8.3/950822.1) id PAA04962; Thu, 4 Dec 1997 15:06:30 -0500 (EST) From: Received: by gatekeeper3.monsanto.com; id OAA08389; Thu, 4 Dec 1997 14:05:54 -0600 Received: from nplxsl01.monsanto.com(164.144.252.39) by gatekeeper3.monsanto.com via smap (3.2) id xma022851; Thu, 4 Dec 97 13:58:01 -0600 Received: by nplxsl01.monsanto.com (NPlex 1.3.167); 4 Dec 1997 13:57:53 -0600 To: chemistry-request@www.ccl.net, armel@fluo.univ-lemans.fr, dpendle@isinet.com cc: chemistry@www.ccl.net Subject: Re: CCL:G:MJS Dewar died October 10 Message-Id: <"1204182215-Re: CCL:G:MJS Dewar died October 10"@MHS> Date: 04 Dec 1997 11:08:20 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Wei Li, I, too, was surprised to not see Allinger's name in the top 50. He is on the list of top 1000 at #374. The important thing to note about the list is that it included references to papers published subsequent to most of the seminal 1977-1980 MM2 papers, and thus does not include their influence directly. I think the literature analyses that Don Boyd has published in the Reviews in Computational Chemistry series capture the impact of Lou's work more clearly. It was exciting, however, to note the number of top 20 authors whose main contributions are the domain of computational chemistry (nearly 50%!!). If you look at the top 20 list of impact values (ave. citations per paper), you will find several authors whose work in semi-empirical methods and force field development clearly had substantial propagation thoroughout the literature. Allinger does not make this top 20 list due to the timing of the MM2 papers, and the relative high volume of papers he has published during the time period. I think we are all appreciative to David Pendlebury for his effort to produce this informative list, for making it available, and also to Armel for bringing it to the attention of the CCL. Sal +++++++++++++++++ Dr. Salvatore Profeta, Jr. Head, Computational Chemistry Monsanto - Ag Technology 800 N. Lindbergh Blvd. MS-U3E St. Louis, MO 63141 314-694-1563 314-694-1080 (fax) SALVATORE.PROFETA.JR.@monsanto.com ssprof@monsanto.com _______________________________________________________________________________ Subject: CCL:G:MJS Dewar died October 10 Author: chemistry-request@www.ccl.net Date: 12/3/97 10:55 PM Armel, I took a quick look of the list and surprised to find that Allinger, NL is not on the list. I know that his paper on MM2/MM3 are widely cited. In my own experience, I found the work of Allinger, Pople J, and Dewar have most profound and practical impact on the modern computational chemistry. The amount of insight, work, and care that went into the three packages, MM2/MM3, Gaussian, and AMPAC/MOPAC, are just tremondous. It will be of great excitment that they get Nobel prize. It is not too late for Allinger and Pople yet. Armel Le Bail wrote: > > Willie Cui wrote: > > >I share you respect to Prof. Dewar and feel the lost of him passing > >away. > > > >On your message, you raised a very import point that his contribution > >to chemistry worthy of the Nobel prize. I am wondering if computational > >chemistry is overlooked by the Nobel prize committee. > > You may look at the computational chemists performances and try to guess > the next Nobel with the ISI's 1000 Most Cited Chemists list : > http://fluo.univ-lemans.fr:8001/1000chimistes.html > > A kind of Pandora box... > > Armel Le Bail - Universite du Maine - Laboratoire des Fluorures > CNRS UPRESA 6010 - Avenue O. Messiaen - 72085 Le Mans cedex 9 - France > Web : http://fluo.univ-lemans.fr:8001/ > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: armel@fluo.univ-lemans.fr > -- Original Sender From: Address: armel@fluo.univ-lemans.fr > 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 -- Willie Cui voice: 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Road email: info@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: info@microsimulations.com -- Original Sender From: Address: info@microsimulations.com 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 willsd@conrad.appstate.edu Fri Dec 5 14:48:23 1997 Received: from am.appstate.edu for willsd@conrad.appstate.edu by www.ccl.net (8.8.3/950822.1) id NAA11435; Fri, 5 Dec 1997 13:41:51 -0500 (EST) Received: from spd3.appstate.edu (SYSTEM@spd3.appstate.edu [152.10.1.29]) by am.appstate.edu (8.8.8/8.8.8) with ESMTP id NAA11373 for ; Fri, 5 Dec 1997 13:41:52 -0500 (EST) Received: from dft ("port 1677"@dft.chem.appstate.edu) by conrad.appstate.edu (PMDF V5.1-10 #26327) with SMTP id <01IQTEZIL7NC8Y4XES@conrad.appstate.edu> for CHEMISTRY@www.ccl.net; Fri, 5 Dec 1997 13:41:49 DST Date: Fri, 05 Dec 1997 13:41:53 -0500 From: Steve Williams Subject: GAMESS freq calculation error X-Sender: willsd@pop.appstate.edu To: CHEMISTRY@www.ccl.net Message-id: <3.0.32.19971205134153.00a23b40@pop.appstate.edu> MIME-version: 1.0 X-Mailer: Windows Eudora Pro Version 3.0 (32) Content-type: text/plain; charset="us-ascii" Hello GAMESS experts: I am a neophyte GAMESS user, but I have considerable experience with gaussian. In the course of trying to learn how to use GAMESS I did an optimization of CCl4, then tried to use this structure to compute frequencies at the same level (rhf/6-31g*). I am using an (August?) 1996 version of GAMESS that compiled without errors on an SGI O2 running IRIX 6.3. The input was: $CONTRL SCFTYP=RHF RUNTYP=HESSIAN EXETYP=RUN COORD=UNIQUE NZVAR=0 MAXIT=64 $END $SYSTEM TIMLIM=100000 MEMORY=8000000 $END $STATPT OPTTOL=1.0E-4 NSTEP=1000 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 POLAR=POPLE $END $GUESS GUESS=HUCKEL $END $SCF DIRSCF=.FALSE. NPUNCH=0 FDIFF=.TRUE. $END $DATA carbon tetrachloride frequencies at 6-31g* level TD C 6.0 0.0000000000 0.0000000000 0.0000000000 CL 17.0 1.0198346116 1.0198346116 1.0198346116 $END The job seemed to run ok, it did print the fial Hessian matrix, but then ended with these lines: -------------------------------------------------------- NORMAL COORDINATE ANALYSIS IN THE HARMONIC APPROXIMATION -------------------------------------------------------- ATOMIC WEIGHTS (AMU) 1 C 12.00000 2 CL 34.96885 3 CL 34.96885 4 CL 34.96885 5 CL 34.96885 MODES 1 TO 6 ARE TAKEN AS ROTATIONS AND TRANSLATIONS. *** ERROR ***, ATTEMPT TO READ A DAF RECORD THAT WAS NEVER WRITTEN. NREC,LEN= 49 0 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Fri Dec 5 09:20:37 1997 STEP CPU TIME = 0.02 TOTAL CPU TIME = 577.7 ( 9.6 MIN) IS 93 .78 PERCENT OF REAL TIME OF 616.0 7335042 WORDS OF DYNAMIC MEMORY USED IF YOU WANT A CORE FILE, SET COREFL=.TRUE. IN $SYSTEM. Cna anyone provide me with some clues as to what went wrong and how to avoid this problem? Thanks, Steve ***************************************** Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu From lavelle@mbi.ucla.edu Sun Dec 7 05:38:40 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id EAA06066; Sun, 7 Dec 1997 04:54:33 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id BAA60018 for ; Sun, 7 Dec 1997 01:54:34 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA27021; Sun, 7 Dec 1997 01:54:34 -0800 Message-Id: <3.0.32.19971207020301.00a8c3a0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sun, 07 Dec 1997 02:03:02 -0800 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Which is faster Direct SCF or Non-Direct SCF Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Greetings, My system has 192 MB RAM, and up to 5 GB swap with a sustained data throughput of 10MB/s. Using non-direct SCF with 211 basis functions the 2e- integral storage is 2(211)^4 = 3.96 GB. Which is faster Direct SCF or Non-Direct SCF? Thanks Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From lavelle@mbi.ucla.edu Mon Dec 8 22:39:03 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id VAA14412; Mon, 8 Dec 1997 21:52:17 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id RAA62986; Mon, 8 Dec 1997 17:27:17 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA25910; Mon, 8 Dec 1997 17:27:04 -0800 Message-Id: <3.0.32.19971208173550.00a48cc0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 08 Dec 1997 17:36:05 -0800 To: chemistry@www.ccl.net, gamess-users@Glue.umd.edu, hyperchem@hyper.com, support@wavefun.com, info@gaussian.com From: Laurence Lavelle Subject: All-electron basis set higher than 3-21G* for Ni. Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Hi, I have searched various sources for an all-electron basis set higher than 3-21G* for Ni. Does one exist, if so I would appreciate knowing where to find it? Thanks Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From DMaxwell@tbc.com Tue Dec 9 14:39:13 1997 Received: from bastion.tbc.com for DMaxwell@tbc.com by www.ccl.net (8.8.3/950822.1) id NAA19038; Tue, 9 Dec 1997 13:41:30 -0500 (EST) Received: from tbc.com (hub.tbc.com [207.243.182.50]) by bastion.tbc.com (8.8.5/8.8.5) with SMTP id MAA15758 for ; Tue, 9 Dec 1997 12:34:23 -0600 (CST) Message-Id: <199712091834.MAA15758@bastion.tbc.com> Date: Tue, 09 Dec 1997 12:43 -0600 From: "David Maxwell" To: chemistry@www.ccl.net Subject: CCL: Conformational preference of N,N'-dimethyl urea Dear CCL Members, I am running into difficulties with determining the conformational preference for N,N'-dimethyl urea. Based on the force field available in Insight II, I can get a preference for either cis-trans or trans-trans. See table below. Force Field* tt ct Delta E (tt-ct) ======================================================================== cff91 -74.673 -78.743 +4.070 cvff -18.809 -17.001 -1.808 amber -27.845 -27.866 +0.021 esff -40.441 -42.713 +2.272 * All were calculated in InsightII V 95.0 with discover_3. No cutoffs were used. I am fully aware of the problems associated with force fields and parameterization in general, but this seems way too much of a difference for such a simple system. As an added point, I ran this calculation with DGAUSS method in Unichem and found almost no energy difference for the two conformational forms. For this ab initio calculation, I utilized the DZVP basis set with LDA approximation. Is there any consensus as to the conformational preference for this system? I am most interested in experimental or high level ab initio support. Of course, I haven't even brought up the issue of solvation! Thanks in advance for you help. David Maxwell Senior Scientist Texas Biotechnology Corp. ** Please send all comments to: dmaxwell@tbc.com Background: I ran quench dynamics on some larger ureas (CFF91 FF) and found a large preference for cis-trans. I wanted to justify my results, so I turned to a simpler system. On the basis of the N,N'-dimethyl urea results, I now have little confidence in my results for the larger urea. From news@compchem.kiev.ua Tue Dec 9 17:39:15 1997 Received: from burka.carrier.kiev.ua for news@compchem.kiev.ua by www.ccl.net (8.8.3/950822.1) id RAA20136; Tue, 9 Dec 1997 17:15:09 -0500 (EST) Received: from sivka.carrier.kiev.ua (root@sivka.carrier.kiev.ua [193.193.193.101]) by burka.carrier.kiev.ua (8.8.6/8.Who.Cares) with ESMTP id XAA20836 for ; Tue, 9 Dec 1997 23:41:46 +0200 (EET) Received: (from uucp@localhost) by sivka.carrier.kiev.ua (8.8.7/8.8.7) with UUCP id XAA17119 for chemistry@www.ccl.net; Tue, 9 Dec 1997 23:38:54 +0200 (EET) Received: (from news@localhost) by netmaster.compchem.kiev.ua (8.7.6/8.6.9) id XAA28149; Tue, 9 Dec 1997 23:10:08 +0200 To: chemistry@www.ccl.net Path: news From: Andrey V Khavryutchenko Newsgroups: compchem.ccl Subject: Titanium and iron parameters for semiempirical methods Date: 09 Dec 1997 23:10:08 +0200 Organization: Computational Chemistry Group Lines: 15 Sender: akhavr@compchem.kiev.ua Message-ID: NNTP-Posting-Host: netmaster.compchem.kiev.ua X-Newsreader: Gnus v5.4.37/XEmacs 19.15 Hi, fellow compchemers! I am looking for Ti and Fe parameters for AM1/PM3/NDDO methods group. CCL archives search resulted in one pointer to the WaveFunction, Inc. ftp site, but it seems not providing them anymore. Can anyone share his parameters sets, links to those or just the experience of calculation of Ti-and Fe-containing systems with semiempirical methods. Note: I focus mainly on inorganic compounds. Thanks in advance. -- SY, Andrey V Khavryutchenko Speaking only for myself From ccl@www.ccl.net Thu Dec 11 01:39:31 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id BAA26828; Thu, 11 Dec 1997 01:39:27 -0500 (EST) Received: from jason05.u.washington.edu for mathomps@u.washington.edu by bedrock.ccl.net (8.8.6/950822.1) id BAA08431; Thu, 11 Dec 1997 01:39:26 -0500 (EST) Received: from saul4.u.washington.edu (mathomps@saul4.u.washington.edu [140.142.83.2]) by jason05.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.05) with ESMTP id WAA42102 for ; Wed, 10 Dec 1997 22:39:26 -0800 Received: (from mathomps@localhost) by saul4.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.04) id WAA09312 for chemistry@ccl.net; Wed, 10 Dec 1997 22:39:25 -0800 (PST) Date: Wed, 10 Dec 1997 22:39:25 -0800 (PST) From: Mark Thompson Message-Id: <199712110639.WAA09312@saul4.u.washington.edu> To: chemistry@ccl.net Subject: C version of LAPACK and multithreading Has anyone tried to run any multi-threaded calculations using CLAPACK? While the code is fast, it appears to very unfriendly for multithreading on Windows NT systems. (lots of statics and externs). While making code thread-safe for NT is not terribly difficult, the sheer number of files I would have to touch and number of statics I'd have to edit just for the matrix diagonalization routines alone feels prohibitive to me. Are there any C-versions of EISPACK floating around out there? (before I try f2c myself). Any experiences by others along these lines (and solutions) would be welcome. Mark Thompson From ccl@www.ccl.net Thu Dec 11 12:39:36 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA00889; Thu, 11 Dec 1997 12:34:54 -0500 (EST) Received: from msuvx2.memphis.edu for tcundari@msuvx2.memphis.edu by bedrock.ccl.net (8.8.6/950822.1) id MAA25345; Thu, 11 Dec 1997 12:34:52 -0500 (EST) Received: from schrock.memphis.edu ([141.225.145.43]) by MSUVX2.MEMPHIS.EDU (PMDF V5.1-8 #16781) with SMTP id <01IR1OASE9E89APCV5@MSUVX2.MEMPHIS.EDU> for chemistry@ccl.net; Thu, 11 Dec 1997 11:34:35 CST Date: Thu, 11 Dec 1997 11:31:20 -0600 From: "Thomas R. Cundari" Subject: OLE automation of Chem3D Plus (PC version) X-Sender: tcundari@cc.memphis.edu (Unverified) To: in@"chemistry@ccl.net" Message-id: <1.5.4.32.19971211173120.00662e14@cc.memphis.edu> MIME-version: 1.0 X-Mailer: Windows Eudora Light Version 1.5.4 (32) Content-type: text/plain; charset="us-ascii" Hello, We have just obtained Chem 3D for a Windows PC. In the manual it says that there is an option for OLE automation using C++, Visual Basic, and Excel. We would like to set up a simple program to open a series of files, assign atom types, MM optimize them, and then continue on with the next molecule in the series. Unofrtunately, we have little expertise w/ OLE. I was wondering if anyone had any experience doing this & perhaps a small template program for achieving this. Thanks. Tom Thomas R. Cundari phone:901-678-2629 Associate Professor FAX:901-678-3447 Dept. of Chemistry email:tcundari@cc.memphis.edu University of Memphis secretary:901-678-2622 Memphis, TN 38152-6060 From P.Tieleman@chem.rug.nl Mon Dec 15 13:40:32 1997 Received: from ns1.rug.nl for P.Tieleman@chem.rug.nl by www.ccl.net (8.8.3/950822.1) id NAA21168; Mon, 15 Dec 1997 13:40:27 -0500 (EST) Received: from rugch4.chem.rug.nl by mailhost with SMTP (XT-PP) with ESMTP; Mon, 15 Dec 1997 19:41:39 +0100 Received: from rugmd10 by rugch4.chem.rug.nl (TAA28323); Mon, 15 Dec 1997 19:40:27 +0100 (MET) Received: (from tieleman@localhost) by rugmd10 (950413.SGI.8.6.12/950213.SGI.AUTOCF) id TAA11782; Mon, 15 Dec 1997 19:40:26 +0100 Date: Mon, 15 Dec 1997 19:40:26 +0100 Message-Id: <199712151840.TAA11782@rugmd10> From: Peter Tieleman To: chemistry@www.ccl.net Subject: continuous distributions of relaxation time Reply-to: P.Tieleman@chem.rug.nl In Comput. Phys. Commun. 27, 213 (1982) Provencher describes a program CONTIN that does all kinds of fits using the principle of parsimony. The program can be used to fit decay functions to a distribution of decay times where simple 2 or 3 parameter fits are impossible. Does anyone know if this program is still around, if it has been translated to fortran 77 (or something newer than fortran 4), and if there is a good alternative? There is a entry CONTIN in netlib but that does something else. Failing information on this program, is there software available to do fitting to noisy decay functions? I'd appreciate any help. regards, Peter Tieleman -- email: tieleman@chem.rug.nl adress: Dept. of Biophysical Chemistry telephone: 31-50-3634338 Nijenborgh 4 fax: 31-50-3634800 9747 AG Groningen The Netherlands From joe@mickey.chem.luc.edu Mon Dec 15 14:05:03 1997 Received: from mickey.chem.luc.edu for joe@mickey.chem.luc.edu by www.ccl.net (8.8.3/950822.1) id NAA21099; Mon, 15 Dec 1997 13:19:41 -0500 (EST) Received: by mickey.chem.luc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id MAA12213; Mon, 15 Dec 1997 12:32:17 -0600 From: joe@mickey.chem.luc.edu (Joseph S Brunzelle) Message-Id: <9712151232.ZM12211@mickey.chem.luc.edu> Date: Mon, 15 Dec 1997 12:32:12 -0600 In-Reply-To: phil stortz "uv software" (Dec 13, 7:39pm) References: <3492D64C.1306@coffey.com> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: pstortz@coffey.com Subject: Re: uv software Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi Phil, Here are the responses that I received about software to calculate uv spectrum: Thank You to all who responded 1. Try ZINDO. Dick C ******************************************************************** Richard A. Caldwell Professor of Chemistry and Dean School of Natural Sciences and Mathematics The University of Texas at Dallas P. O. Box 830688 Richardson TX 75083-0688 caldwell@utdallas.edu (972)-883-2516 or (972)-883-2906 (972)-883-6371 or (972)-883-2925 Fax ********************************************************************** 2. See the evaluation copy of HyperChem 5 at www.hyper.com. Zindo/S in this package is specifically parameterized for spectroscopy. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: joe@mickey.chem.luc.edu [SMTP:joe@mickey.chem.luc.edu] Sent: Tuesday, November 18, 1997 2:19 PM To: chemistry@In order to: 3. calculate uv spectrum of some cmpds? I would recommend Michael Zerner's, semiempirical, ZINDO program. It is available commercially from Oxford Molecular and from MSI, and can handle fairly large molecules. (ZINDO is not so good at coming up with good geometries, however, and you would need an optimized geometry first. I would recommend something like MOPAC or DFT for the geometry optimization, then ZINDO for the UV calculation.) The implementation of ZINDO in Oxford Molecular's CAChe software is particularly nice, because it will construct the UV spectrum from the absorbances, and then you can see which transition (which orbitals are involved) is responsible for each peak by simply clicking on the appropriate part of the spectrum. EC --- Ernest Chamot Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, IL 60540 (630) 637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl www.ccl.net 4. UV absorption band can be calculated from Spartan semiempirical module with CI calculation. First run AM1 geometry optimization then run a single point energy calculation with option keyword "CI" and "printlev=2". --Wayne -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemistry | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ 4. I would recomend that you use a system based upon the PPP SCF MO method. There are commercial implementations of this method around, for instance PISYSTEM, which runs through Windows. My research involves the use of molecular modeling for dyestuff design, and nothing else that I have tried has been as good at predicting UV-Vis spectra. Zindo only works for simple dyes, such as polyene series and cyanine series. What kinds of compounds are you looking at? Jason _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "Too much of a North Carolina State University, | good thing is wonderful" Raleigh, N.C. 27695 - 8301 | | - Mae West. Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ -- ------------------------------------------------------------------------ Joseph S. Brunzelle (joe@mickey.chem.luc.edu) Loyola University of Chicago Dept. of Chemistry Chicago, IL 60626 Tel. 773-508-3132 Fax. 773-508-3086 ------------------------------------------------------------------------- From info@microsimulations.com Mon Dec 15 20:40:35 1997 Received: from maple.nis.net for info@microsimulations.com by www.ccl.net (8.8.3/950822.1) id UAA23256; Mon, 15 Dec 1997 20:20:55 -0500 (EST) Received: from merlin.nis.net by maple.nis.net with smtp (Smail3.2.0.95 #47) id m0xhmVj-0010F2C; Mon, 15 Dec 1997 21:13:27 -0500 (EST) Received: from PACKARDBELL1 [207.99.101.97] by merlin.nis.net with smtp (Exim 1.62 #1) id 0xhmPw-0007rv-00; Mon, 15 Dec 1997 21:07:29 -0500 Message-ID: <349600DE.3880@microsimulations.com> Date: Mon, 15 Dec 1997 20:17:34 -0800 From: Willie Cui Reply-To: info@microsimulations.com Organization: microsimulations X-Mailer: Mozilla 3.0 (Win95; I; 16bit) MIME-Version: 1.0 To: SALVATORE.PROFETA.JR@monsanto.com CC: chemistry-request@www.ccl.net, armel@fluo.univ-lemans.fr, dpendle@isinet.com, chemistry@www.ccl.net Subject: Re: CCL:Re: CCL:G:MJS Dewar died October 10 References: <"1204182215-Re: CCL:G:MJS Dewar died October 10"@MHS> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sal, I completely agree with you on your analysis of the citation situation, and share your appreciation to David and Armel. All the best! SALVATORE.PROFETA.JR@monsanto.com wrote: > > Wei Li, > > I, too, was surprised to not see Allinger's name in the top 50. He is > on the list of top 1000 at #374. The important thing to note about the > list is that it included references to papers published subsequent to > most of the seminal 1977-1980 MM2 papers, and thus does not include > their influence directly. I think the literature analyses that Don Boyd > has published in the Reviews in Computational Chemistry series capture > the impact of Lou's work more clearly. > > It was exciting, however, to note the number of top 20 authors whose > main contributions are the domain of computational chemistry (nearly > 50%!!). If you look at the top 20 list of impact values (ave. citations > per paper), you will find several authors whose work in semi-empirical > methods and force field development clearly had substantial propagation > thoroughout the literature. Allinger does not make this top 20 list due > to the timing of the MM2 papers, and the relative high volume of papers > he has published during the time period. > > I think we are all appreciative to David Pendlebury for his effort to > produce this informative list, for making it available, and also to > Armel for bringing it to the attention of the CCL. > > Sal > +++++++++++++++++ > Dr. Salvatore Profeta, Jr. > Head, Computational Chemistry > Monsanto - Ag Technology > 800 N. Lindbergh Blvd. MS-U3E > St. Louis, MO 63141 > 314-694-1563 > 314-694-1080 (fax) > SALVATORE.PROFETA.JR.@monsanto.com > ssprof@monsanto.com > > > > _______________________________________________________________________________ > Subject: CCL:G:MJS Dewar died October 10 > Author: chemistry-request@www.ccl.net > Date: 12/3/97 10:55 PM > > Armel, > > I took a quick look of the list and surprised to find that Allinger, NL > is not on the list. I know that his paper on MM2/MM3 are widely cited. > > In my own experience, I found the work of Allinger, Pople J, and Dewar > have most profound and practical impact on the modern computational > chemistry. The amount of insight, work, and care that went into the > three packages, MM2/MM3, Gaussian, and AMPAC/MOPAC, are just tremondous. > It will be of great excitment that they get Nobel prize. > It is not too late for Allinger and Pople yet. > > Armel Le Bail wrote: > > > > Willie Cui wrote: > > > > >I share you respect to Prof. Dewar and feel the lost of him passing > > >away. > > > > > >On your message, you raised a very import point that his contribution > > >to chemistry worthy of the Nobel prize. I am wondering if computational > > >chemistry is overlooked by the Nobel prize committee. > > > > You may look at the computational chemists performances and try to guess > > the next Nobel with the ISI's 1000 Most Cited Chemists list : > > http://fluo.univ-lemans.fr:8001/1000chimistes.html > > > > A kind of Pandora box... > > > > Armel Le Bail - Universite du Maine - Laboratoire des Fluorures > > CNRS UPRESA 6010 - Avenue O. Messiaen - 72085 Le Mans cedex 9 - France > > Web : http://fluo.univ-lemans.fr:8001/ > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: armel@fluo.univ-lemans.fr > > -- Original Sender From: Address: armel@fluo.univ-lemans.fr > > 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 > > -- > Willie Cui voice: 201-512-0486 > MicroSimulations fax: 201-512-0489 > 478 Green Mountain Road email: info@microsimulations.com > Mahwah, NJ 07430 URL: http://www.microsimulations.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: info@microsimulations.com > -- Original Sender From: Address: info@microsimulations.com > 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 > > --- > Administrivia: This message is automatically appended by the mail exploder: > 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 > --- -- Willie Cui voice: 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Road email: info@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com