From chemistry-request@server.ccl.net Wed Dec 30 05:04:21 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA15190 for ; Wed, 30 Dec 1998 05:04:21 -0500 Received: from iris.inc.bme.hu (iris.inc.bme.hu [152.66.63.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA07449 Wed, 30 Dec 1998 04:58:29 -0500 (EST) Received: from localhost (dino@localhost) by iris.inc.bme.hu (8.9.1/8.9.1) with ESMTP id KAA12126 for ; Wed, 30 Dec 1998 10:58:24 +0100 (BUD) Date: Wed, 30 Dec 1998 10:58:23 +0100 From: Szieberth Denes To: chemistry@www.ccl.net Subject: 2GB limit Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone, I'm just trying to set up a Linux box for G94 calculations, and I have some questions which I hope someone can answer. The maximum file size in e2fs (as far as I know) is 2 GB. The only way I could do calculations requiring bigger rwf files was to divide the rwf into several parts. I had, however, the problem again, that I have a 18 GB partition, and the input line for gaussian to utilize 9 rwf files is too long for the input parser, and I couldn't get gaussian to accept more than one %rwf input line. Does anyone know some other way to work around the 2 GB problem or what syntax should I use in the G94 input? regards and happy new year, Denes Szieberth dino@iris.inc.bme.hu From chemistry-request@server.ccl.net Wed Dec 30 07:40:06 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA15241 for ; Wed, 30 Dec 1998 07:40:06 -0500 Received: from hermes.aston.ac.uk (hermes.aston.ac.uk [134.151.79.46]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA11526 Wed, 30 Dec 1998 07:34:14 -0500 (EST) Received: from pharm78100.aston.ac.uk (pharm7145.aston.ac.uk) [134.151.78.100] by hermes.aston.ac.uk with smtp (Exim 1.82 #3) id 0zvKsI-0004Ll-00; Wed, 30 Dec 1998 12:37:18 +0000 Comments: Authenticated sender is From: "chaudash@aston.ac.uk" Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Wed, 30 Dec 1998 12:36:49 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: BIDS TO ENDNOTE Reply-to: @aston.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-Id: Hi ccl'ers, I have a program for managing references called Endnote. Apparently there is a way of putting bids searches directly into the program, however I do not know how. I would be most grateful if someone would enlighten me on how to do this. Many thanks and have a great new year. Shaqil From chemistry-request@server.ccl.net Wed Dec 30 11:08:58 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15297 for ; Wed, 30 Dec 1998 11:08:57 -0500 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA17796 Wed, 30 Dec 1998 11:03:05 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with ESMTP id LAA10342; Wed, 30 Dec 1998 11:03:00 -0500 (EST) Received: (from shenkin@localhost) by still3.chem.columbia.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA18807; Wed, 30 Dec 1998 11:03:00 -0500 (EST) Date: Wed, 30 Dec 1998 11:03:00 -0500 (EST) From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199812301603.LAA18807@still3.chem.columbia.edu> To: "E. Lewars" , "J. Sichel" Subject: Re: CCL:RATE CONSTANT AND BARRIER-QUESTION Cc: chemistry@www.ccl.net > From chemistry-request@www.ccl.net Tue Dec 29 15:33:52 1998 > On Mon, 28 Dec 1998, E. Lewars wrote: > > > True or false: > > > > Two reactions with exactly the same free energies of activation (delta G > > of activation, not Arrhenius activation energy) _must_ have the same > > rate constants (at the same temperature). > > I can think of two reasons why not. > 1. The transition-state-theory expression for k includes a barrier > transmission coefficent (denoted by kappa) which may vary between > reactions. > 2. Transition-state theory may not be exact for the reactions in question. It is partly a matter of definition. If one accepts the definition: k_rate = ( k_boltz * T / h_bar ) exp( -DG_act / RT ) then, by definition, k_rate and DG_act are functionally related and of course any two reactions with the same DG_act must have the same k_rate. I think this is the answer most people would accept. In this picture, DG_act is the value the activation free energy would have if the theory were valid. If the theory is invalid, then the underlying physical picture would be misleading. For instance, if T-variation studies were performed in which DG_act were dissected into a DH_act and a DS_act, the DH_act would not really correspond to the enthalpy difference between reactants and transition state on some PE surface. OTOH, if DG_act is computed by some other means, such as by an exact classical calculation on an exactly correct potential-energy surface, then in fact the above equation will be correct only to the extent that transition-state theory (or, ahem, activated-complex theory) is applicable. For example, where tunnelling is important, the k_rate calculated from the computed DG_act would be much smaller than the experimental k_rate. -P. *** "Freedom's just another word for nothing left to lose." (B. Yeltsin)*** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* * MacroModel URL: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html * From chemistry-request@server.ccl.net Wed Dec 30 15:48:26 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA15413 for ; Wed, 30 Dec 1998 15:48:25 -0500 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA01973 Wed, 30 Dec 1998 15:42:30 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.1a/8.9.1) with ESMTP id UAA23211 for ; Wed, 30 Dec 1998 20:43:58 GMT Date: Wed, 30 Dec 1998 20:43:47 +0000 From: Michael Nolan To: ccl Subject: [cbas25@strath.ac.uk: CCL:Linux vs WindowsNT vs Windows95] Message-ID: <19981230204347.C304@rennes.nmrc.ucc.ie> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.94.15i >Dear CCL community, ---snip--- >Worrying too is the move being made by SGI (who have hitherto been >the providers of high-end hardware for computational chemistry) to adopt >WindowsNT as an OS (I think that I am reminded of the Blackwidow spider >which eats its mate after mating). It's not just SGI. HP have also done and are doing the same thing. I would assume that DEC will go the same way, if they haven't already. This leaves, and correct me if I am wrong, SUN as the only company manufacturing workstations with their own processors and OS Will we be all using Windows based OSs in the future? regards Michael -- ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html EMRS Call for papers: http://nmrc.ucc.ie/groups/AMT/SympMain.html **************************************************************************** From chemistry-request@server.ccl.net Wed Dec 30 20:51:51 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA16187 for ; Wed, 30 Dec 1998 20:51:51 -0500 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id UAA05944 Wed, 30 Dec 1998 20:45:43 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA07958; Thu, 31 Dec 98 09:19:16 -0800 Date: Thu, 31 Dec 1998 09:19:16 -0800 (PST) From: Fenglou Mao To: Michael Nolan Cc: ccl Subject: Re: CCL:[cbas25@strath.ac.uk: Linux vs WindowsNT vs Windows95] In-Reply-To: <19981230204347.C304@rennes.nmrc.ucc.ie> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 30 Dec 1998, Michael Nolan wrote: > >Worrying too is the move being made by SGI (who have hitherto been > >the providers of high-end hardware for computational chemistry) to adopt > >WindowsNT as an OS (I think that I am reminded of the Blackwidow spider > >which eats its mate after mating). > > It's not just SGI. HP have also done and are doing the same thing. I would assume that DEC will go the same way, if they haven't already. This leaves, and correct me if I am wrong, SUN as the only company manufacturing workstations with their own processors and OS > Will we be all using Windows based OSs in the future? > But I think WindowsNT's performance and reliability are much lower than UNIX. Dr. Watson offen go out to report some problem. Then your application is closed and you lost all you have done. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@server.ccl.net Wed Dec 30 22:17:40 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA16454 for ; Wed, 30 Dec 1998 22:17:40 -0500 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA06114 Wed, 30 Dec 1998 22:11:41 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with ESMTP id WAA03808; Wed, 30 Dec 1998 22:11:28 -0500 (EST) Received: (from shenkin@localhost) by still3.chem.columbia.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) id WAA20076; Wed, 30 Dec 1998 22:11:28 -0500 (EST) Date: Wed, 30 Dec 1998 22:11:28 -0500 (EST) From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199812310311.WAA20076@still3.chem.columbia.edu> To: ccl , Michael Nolan Subject: Re: CCL:[cbas25@strath.ac.uk: Linux vs WindowsNT vs Windows95] Cc: +ccl@still3.chem.columbia.edu > From chemistry-request@www.ccl.net Wed Dec 30 16:52:50 1998 > >Worrying too is the move being made by SGI (who have hitherto been > >the providers of high-end hardware for computational chemistry) to adopt > >WindowsNT as an OS (I think that I am reminded of the Blackwidow spider > >which eats its mate after mating). Bear in mind that SGI will be supporting NT at the low end but only UNIX at the high end. They have also just joined LINUX International. This might give some hint as to what their future intentions are. > It's not just SGI. HP have also done and are doing the same thing. Of course; IA64 is a joint HP/Intel project and has been from the start. > I would assume that DEC will go the same way, if they haven't already. Well, DEC's Alpha chip already supports UNIX, Linux, NT and OpenVMS. Their buyout by Compaq makes them manufacturers of both Intel and Alpha-based machines, but they show no signs of abandoning Alpha. > This leaves, and correct me if I am wrong, SUN as the only company > manufacturing workstations with their own processors and OS > Will we be all using Windows based OSs in the future? You are wrong on several counts. First, Sun has announced Solaris support for IA64, though they've not announced any plans to build machines around this chip. Second, IBM has announced neither plans to port AIX to IA64, nor any plans to build machines based on this chip architecture; they seem committed to the PPC architecture. (The recently announced Power3 architecture is a PPC architecture.) Third, none of the UNIX-based companies has announced plans to abandon UNIX. AFAIK, the situation several years from now will be as follows, based on what companies have announced so far. This could change, and in addition all this is from memory and some could be wrong even now: Hardware OS SGI Intel Windows (low end), IRIX (high end) HP Intel Windows / HPUX Sun SPARC Solaris IBM PPC AIX DEC Alpha Windows / Linux / OSF-UNIX / OpenVMS If I'm not mistaken, MicroSoft has announced that several years from now there will be a merged product called Windows 2000 -- NT-5 will never be released. Thus I'm using Windows as a generic term. Also, we may see the same sort of consolidation in the UNIX OS world that we're seeing in hardware. For instance, Sun is making a push for Solaris to be the standard by supporting Intel now and planning support into the future for IA64, even though they evidently don't plan to build Intel-based machines. Can Solaris, IRIX, HPUX, AIX, OSF-UNIX all survive separately, any more than SPARC, MIPS, PA/RISC, rs/6000, ppc and Alpha could survive separately? For all I know, maybe we'll see IRIX, HPUX, etc., disappearing in favor of Linux and one or two others, like AIX -- who knows? (Hint -- I don't.) Based on announcements so far, there is more consolidation on the hardware than on the software front. As Mark Twain cabled from London upon reading his obituary in a New York newspaper, "The reports of my death are greatly exaggerated." UNIX could say the same of various recent announcements on CCL. In fact, we live in interesting times. Several years ago the pundits were predicting that we'd all be living in a Windows world today. It didn't happen, and though some think it will still happen, what in fact is happening is that hardware, not software, is driving the changes that are taking place. All of a sudden Linux is gaining acceptance in places which previously saw Windows as their most likely alternative. This is only because of fast, cheap Intel-based platforms. It has nothing to do with Windows, and is in fact a threat to Windows. The report here that SGI is "adopting" NT, while correct as far as it goes, is not comprehensive. They are *adding* NT, not deserting UNIX. And, in fact, though computational chemists have been slow to adopt Windows, there has been a mass defection from UNIX to NT in some critical scientific/engineering disciplines -- especially CAD/CAM. SGI hopes that by bringing hardware and software excellence to an NT platform with their VPC, they can recapture some of that market. In the meantime, I don't think computational chemists will have anything to cry about, particularly if Linux should become available on that machine. There are some who think UNIX is doomed and that Windows is the world of the future. I respect those people, and I have no problem with chemists who want to use Windows (in its various incarnations), or with developers who want to write computational-chemistry software for Windows, or with manufacturers who want to build fast machines that run Windows. Though some people see whatever trend there is toward Windows as the elimination of choice and diversity, what has really happened so far is the opposite, at least in computational chemistry. For the first time, one can run "real" computation-chemistry software on something other than UNIX, as well as on UNIX. To me, that sounds like *more* choice, not less. On the other hand (and I'll admit to being a contrarian), I doubt the premise that UNIX is doomed. I think UNIX (Linux, especially) presents at least as great a threat to Windows as Windows does to UNIX. However, it is Windows that made Intel-based machines mass-market commodities, and it is this, in turn, that drives the move away from other hardware architectures and that motivates the great support that Linux (for example) provides for Intel. -P. *** "Freedom's just another word for nothing left to lose." (B. Yeltsin)*** *Peter Shenkin; Chemistry, Columbia U.; shenkin@columbia.edu (212)854-5143* * MacroModel URL: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html * From chemistry-request@server.ccl.net Wed Dec 30 23:25:35 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA16516 for ; Wed, 30 Dec 1998 23:25:34 -0500 Received: from MIT.EDU (PACIFIC-CARRIER-ANNEX.MIT.EDU [18.69.0.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA06280 Wed, 30 Dec 1998 23:19:34 -0500 (EST) Received: from DEPARTMENT-OF-ALCHEMY.MIT.EDU by MIT.EDU with SMTP id AA25119; Wed, 30 Dec 98 23:19:37 EST Received: by department-of-alchemy.mit.edu (8.8.7/4.7) id XAA07205; Wed, 30 Dec 1998 23:19:37 -0500 (EST) Message-Id: <199812310419.XAA07205@department-of-alchemy.mit.edu> To: Chemistry@www.ccl.net Subject: Cerius2/Gaussview Date: Wed, 30 Dec 1998 23:19:37 EST From: Ning Xie Hi,there, Is there anybody ever compared Cerius2 with Gaussview? I've never had a chance to try out Gaussview but I was told that it is "thumb down". However I am not so amazed by Cerius2 either. It is kinda difficult for me to decide which to buy in combination with Gaussian 98. Thank you for your time and HAPPY NEW YEAR! -------------------------------------------------------------------------- | Ning Xie, Post-doctoral Associate e-mail: ningxie@mit.edu | | Chemical Engineering Department ning_xie@yahoo.com | | Massachusetts Institute of Technology Fax: (617)253-6534 | | 66-057, 77 Massachusetts Avenue Tel: (617)253-6535 (O) | | Cambridge, MA 02139-4307, USA (781)245-7954 (H) | --------------------------------------------------------------------------