From korkin@act.sps.mot.com Fri Apr 10 02:23:37 1998 Received: from spsem02.sps.mot.com for korkin@act.sps.mot.com by www.ccl.net (8.8.3/950822.1) id BAA28984; Fri, 10 Apr 1998 01:26:55 -0400 (EDT) Received: from mogate.sps.mot.com by spsem02.sps.mot.com (4.1/SMI-4.1/Email 2.1 10/25/93) id AA20883 for chemistry@www.ccl.net; Thu, 9 Apr 98 22:26:54 MST Received: from emailsps.sps.mot.com by mogate.sps.mot.com (4.1/SMI-4.1/Email-2.0) id AA11982 for chemistry@www.ccl.net; Thu, 9 Apr 98 22:26:53 MST Received: from zsneezy.sps.mot.com (korkin@zsneezy [223.189.20.100]) by sps.mot.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id WAA17467 for ; Thu, 9 Apr 1998 22:26:52 -0700 (MST) From: Anatoli Korkin Received: (from korkin@localhost) by zsneezy.sps.mot.com (8.8.6/8.8.6) id WAA16364 for chemistry@www.ccl.net; Thu, 9 Apr 1998 22:26:51 -0700 (MST) Date: Thu, 9 Apr 1998 22:26:51 -0700 (MST) Message-Id: <199804100526.WAA16364@zsneezy.sps.mot.com> To: chemistry@www.ccl.net Subject: molecular mechanics for material mechanical properties X-Mailer: Siren Mail (Motif 2.02 95/05/15) Mime-Version: 1.0 Content-Id: <304_14957_892186011_17@zsneezy> Content-Type: text/plain; charset="us-ascii" Dear Colleagues, This questions can be naive or obscure, since I am not familiar with the field. Are molecular mechanics applications for computing material mechanical properties (well) known? Like elasticity, stress, etc. Can someone point good papers, reviews, books, if any, and also the programs and type of parameters, which are particularly good for these purposes. Thank you for you consideration, Anatoli Korkin From gran@classic.chem.msu.su Fri Apr 10 05:23:52 1998 Received: from classic.chem.msu.su for gran@classic.chem.msu.su by www.ccl.net (8.8.3/950822.1) id FAA29832; Fri, 10 Apr 1998 05:06:16 -0400 (EDT) From: Received: from classic ( [158.250.32.143] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Fri, 10 Apr 1998 13:05:47 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-Id: <199803101305.4725548.7@classic.chem.msu.su> Return-receipt-to: gran@classic.chem.msu.su Date: Fri, 10 Apr 98 13:05:38 +0400 To: CHEMISTRY@www.ccl.net In-Reply-To: <35204B41.CC401C06@email.psu.edu> Subject: Re: Summary: Linux versus win NT X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.27c (Unregistered) Dear netters, Taking into account the recent CCL discussion, this letter, which contains some comments on the motivation and goals of our PC GAMESS project, probably may be interesting for the computational chemists community. Please, note, this letter is intended solely to clarify our own position. It is not intended to initiate useless discussions on "what is the best operating system?" or, more globally, "what is the essense of life?" topics. > I have been using the windows version of gamess for almost 6 > months > now and i have had no problems. I still see people trying to > install > gamess under linux. > Is there a good reason why people are still using gamess under > linux on PC's ? Are there any serious problems or bugs in the > windows > version ? >I expected to get a word from Dr Alex. A. Granovsky who ported gamess to >win95/nt or from the gamess group , but i didn't . It seems that they are as >anxious >as i am to hear the comments of the users before they say anything. The main goal of the PC GAMESS project was (and currently is) to use high level Intel-based workstations as promising production systems for serious and intensive quantum chemical calculations. There is an old tradition to use UNIX on the workstation-class computers designated mainly (or exclusively) for various scientific calculations. On the other hand, the world of PC is a relatively new and still partially unknown area (although, for example, our group has used them since at least 1992 in the production work) for the most of the computation chemists. This is exactly the case when the old good receipts are not necessarily the best ones. Here, a very careful choice of the operating system to be used and the corresponding software available (e.g. compilers) is critical, if somebody is really interested in getting the good production performance. Unfortunately, this simple and important idea is rarely considered as seriously as probably should be. The correct choice plays the decisive role as really allowing the Intel-based systems to be competitive with other modern hardware platforms (DEC, SGI, IBM, etc..). To our opinion, a thorough analysis of the current situation with the PC operating systems and compilers available shows that the usage of free UNIX clones (like Linux, FreeBSD, etc...) on the production level systems still has serious drawbacks. The freely available gcc/f2c and g77 compilers (and their clones) are certainly not capable to generate an optimized floating point code of the required quality. Though there exist several commercial Linux-based Fortran and C compilers of higher quality, there are still other serious problems with them, such as the code stability, overoptimization, bad optimization, and so on. In general, the situation is not surprising, because Linux is still a relatively new area in the (scientific-oriented) compiler market. Today, the situation with the non-UNIX software is much better. There is a lot of high quality compilers available, mainly for Win32 (Win NT and 95). Windows NT itself is stable, fast, and powerful enough to run efficiently the most demanding scientific programs, including various quantum chemistry packages. It has the built-in support of SMP. If needed, there is a variety of useful (both free and commercial) software on the market (e.g., telnet daemons, full POSIX support, UNIX compatibility tools, etc...), which simplifies the process of transition from the UNIX to the NT environment. This was (and still is) the motivation for our decision to use Windows NT as the base system for the PC GAMESS project and for our production computers (though the PC GAMESS itself is available also for other PC operating systems, including Windows 95, OS/2, and even DOS). According to our estimates, there are already about 200-400 persons in the world, who use the PC GAMESS in their production work. We think this is large enough. Just to sum up: On the PC, there are multiple reasons to work under Linux. There are also multiple reasons to use NT instead. Both systems have serious advantages (and disadvantages as well) as compared to each other. Both of them will definitely survive in the forthcoming millennium. Both are stable, powerful, and have the prospects for the further growth. For the intensive scientific calculations, NT still seems to be a better choice. Possibly, the situation will change in future. Possibly, it won't. In any case, this process may take up to several years. But we are interested to get the results of our calculations today. Yours sincerely, Alex. A. Granovsky, Laboratory of Chemical Cybernetics, Moscow State University All information concerning the current status of the PC GAMESS project can be found on the http://classic.chem.msu.su/gran/gamess/index.html From charwel@chrs1.chem.lsu.edu Fri Apr 10 10:23:41 1998 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id JAA01213; Fri, 10 Apr 1998 09:34:07 -0400 (EDT) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA25488; Fri, 10 Apr 1998 08:32:23 -0500 Date: Fri, 10 Apr 1998 08:32:23 -0500 (CDT) From: Chris Harwell Reply-To: Chris Harwell Cc: beuwulf list , Gamess user list , ccl Subject: Re: CCL:Summary: Linux versus win NT for running GAMESS In-Reply-To: <199803101305.4725548.7@classic.chem.msu.su> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 10 Apr 1998 gran@classic.chem.msu.su wrote: > > Dear netters, > letter is intended solely to clarify our own position. It is not intended to > initiate useless discussions on "what is the best operating system?" - snip - good > > Is there a good reason why people are still using gamess under > > linux on PC's ? Are there any serious problems or bugs in the > > windows version ? - snip - Wonderful, why don't we try to address the question of speed for this one application and look for some bench marks? Does anyone have a dual boot linux/NT system, both with good compilers that could provide some benchmarks? If someone does, we could then address one part of this -- incredibly interesting and relevant - discussion without being sidetracked! Chris "Everything positive originates in a positive attitude from someone" :> From nakiya@engin.umich.edu Fri Apr 10 11:23:42 1998 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id LAA02013; Fri, 10 Apr 1998 11:13:33 -0400 (EDT) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id LAA01030 for ; Fri, 10 Apr 1998 11:13:35 -0400 (EDT) Date: Fri, 10 Apr 1998 11:13:35 -0400 (EDT) From: Naoko Akiya To: chemistry@www.ccl.net Subject: CCL: MD package In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am looking for an MD package that can do the following: - uses user-supplied potential models as well as built-in models - does isothermal simulation with Nose-Hoover thermostat - works on Unix, preferably HP - calculates free energy - lets the user follow the trajectory of a particular molecule from a given initial condition If you have any suggestions for a particular MD package that does all or some of the above, please let me know. FYI we are not looking into polymers or macromolecules. I will summarize the responses if there is any interest. Thank you very much. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (734) 764-7121 Ann Arbor, MI 48109-2136 fax (734) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From casero@kali.cox.miami.edu Fri Apr 10 12:23:43 1998 Received: from kali.cox.miami.edu for casero@kali.cox.miami.edu by www.ccl.net (8.8.3/950822.1) id MAA02331; Fri, 10 Apr 1998 12:00:23 -0400 (EDT) Received: from localhost by kali.cox.miami.edu (AIX 3.2/UCB 5.64/4.03) id AA12775; Fri, 10 Apr 1998 12:01:36 -0400 Date: Fri, 10 Apr 1998 12:01:35 -0400 (EDT) From: Juan Jose Casero To: Chris Harwell , Gamess user list Cc: beuwulf list , ccl Subject: Re: GU: Re: CCL:Summary: Linux versus win NT for running GAMESS In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 10 Apr 1998, Chris Harwell wrote: Great! I would love to see the benchmarks myself. From my sig line below it should come as no surprise that I am a Linux advocate. However, unlike some others I don't particularly much care for flaming. Cheers....... > > On Fri, 10 Apr 1998 gran@classic.chem.msu.su wrote: > > > > Dear netters, > > letter is intended solely to clarify our own position. It is not intended to > > initiate useless discussions on "what is the best operating system?" > - snip - > good > > > > Is there a good reason why people are still using gamess under > > > linux on PC's ? Are there any serious problems or bugs in the > > > windows version ? > - snip - > > Wonderful, why don't we try to address the question of speed for this > one application and look for some bench marks? > > Does anyone have a dual boot linux/NT system, both with good compilers > that could provide some benchmarks? > > If someone does, we could then address one part of this -- > incredibly interesting and relevant - discussion without being > sidetracked! > > Chris > "Everything positive originates in a positive attitude from someone" :> > > > > Juan Casero ------------------------------------------------------------------------- Evanseck Research Group Department of Chemistry University of Miami Coral Gables, Florida email: casero@kali.cox.miami.edu ------------------------------------------------------------------------- __ _ / / (_)__ __ ____ __ / /__/ / _ \/ // /\ \/ / . . . t h e c h o i c e o f a /____/_/_//_/\_,_/ /_/\_\ G N U g e n e r a t i o n . . . From greg@nano.chem.nwu.edu Fri Apr 10 13:23:43 1998 Received: from nano.chem.nwu.edu for greg@nano.chem.nwu.edu by www.ccl.net (8.8.3/950822.1) id MAA02533; Fri, 10 Apr 1998 12:30:24 -0400 (EDT) Received: from nano.chem.nwu.edu ([129.105.14.190]) by nano.chem.nwu.edu (WESMTP 1.4397) with SMTP id 662970718; Fri, 10 Apr 1998 16:35:13 GMT Date: Fri, 10 Apr 1998 11:35:12 -0500 From: "G. Rechtsteiner" Subject: Fundamentals To: CHEMISTRY@www.ccl.net X-Sender: greg@nano.chem.nwu.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: <662972203@nano.chem.nwu.edu> Hello: I was wondering if anyone knows of a software package (freeware or other) that has an algorithm for working out fundamentals, combinations, and overtones from an input of a series of experimental peaks from an IR or Raman spectrum. Thank you for your time and bandwidth, Greg -- Greg Rechtsteiner Norwestern University Department of Chemistry 2145 Sheridan Rd. Evanston, IL 60208 From kotelyan@plmsc.psu.edu Fri Apr 10 13:27:37 1998 Received: from plmsc.psu.edu for kotelyan@plmsc.psu.edu by www.ccl.net (8.8.3/950822.1) id NAA02817; Fri, 10 Apr 1998 13:20:34 -0400 (EDT) Received: (from kotelyan@localhost) by plmsc.psu.edu (8.8.2/8.8.2) id NAA23278; Fri, 10 Apr 1998 13:20:23 -0400 (EDT) Date: Fri, 10 Apr 1998 13:20:21 -0400 (EDT) From: Mike Kotelyanskii To: Chris Harwell cc: beuwulf list , Gamess user list , ccl Subject: Re: CCL:Summary: Linux versus win NT for running GAMESS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Well, I happen to have the dual boot Win95/Linux system. No compilers on Win95, sorry, and usual gnu stuff on Linux (for the obvious reason), so if there is a possibility to get a executable I could volunteer and run tests. I do not use GAMESS myself, but I hope I'll be able to run some tests if the some kind of README/HowTo/Manual is provided Mike ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan University Park, PA 16802, USA -------------------------------------------------------------------------------- On Fri, 10 Apr 1998, Chris Harwell wrote: > > On Fri, 10 Apr 1998 gran@classic.chem.msu.su wrote: > > > > Dear netters, > > letter is intended solely to clarify our own position. It is not intended to > > initiate useless discussions on "what is the best operating system?" > - snip - > good > > > > Is there a good reason why people are still using gamess under > > > linux on PC's ? Are there any serious problems or bugs in the > > > windows version ? > - snip - > > Wonderful, why don't we try to address the question of speed for this > one application and look for some bench marks? > > Does anyone have a dual boot linux/NT system, both with good compilers > that could provide some benchmarks? > > If someone does, we could then address one part of this -- > incredibly interesting and relevant - discussion without being > sidetracked! > > Chris > "Everything positive originates in a positive attitude from someone" :> > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: charwel@chrs1.chem.lsu.edu > -- Original Sender From: Address: charwel@chrs1.chem.lsu.edu > 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 nakiya@engin.umich.edu Fri Apr 10 14:23:45 1998 Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by www.ccl.net (8.8.3/950822.1) id NAA02938; Fri, 10 Apr 1998 13:31:33 -0400 (EDT) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id NAA01697 for ; Fri, 10 Apr 1998 13:31:34 -0400 (EDT) Date: Fri, 10 Apr 1998 13:31:33 -0400 (EDT) From: Naoko Akiya To: chemistry@www.ccl.net Subject: Re: CCL:MD package In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear All, > > I am looking for an MD package that can do the following: > > - uses user-supplied potential models as well as built-in models > - does isothermal simulation with Nose-Hoover thermostat > - works on Unix, preferably HP > - calculates free energy > - lets the user follow the trajectory of a particular molecule from a > given initial condition I forgot to mention one more thing: - can do multiple timestep integration > If you have any suggestions for a particular MD package that does all > or some of the above, please let me know. FYI we are not looking into > polymers or macromolecules. I will summarize the responses if there is > any interest. > > Thank you very much. > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > Naoko Akiya nakiya@engin.umich.edu > University of Michigan > Dept. of Chemical Engineering phone (734) 764-7121 > Ann Arbor, MI 48109-2136 fax (734) 763-0459 > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Dennis.Salahub@UMontreal.CA Fri Apr 10 16:27:05 1998 Received: from ulys.POSTE.UMontreal.CA for Dennis.Salahub@UMontreal.CA by www.ccl.net (8.8.3/950822.1) id PAA03635; Fri, 10 Apr 1998 15:41:40 -0400 (EDT) Received: from [132.204.70.31] (salahub.CTHEO.UMontreal.CA [132.204.70.31]) by ulys.POSTE.UMontreal.CA with SMTP id PAA14062 (8.6.11/IDA-1.6); Fri, 10 Apr 1998 15:41:40 -0400 Date: Fri, 10 Apr 1998 15:41:40 -0400 Message-ID: <199804101941.PAA14062@ulys.POSTE.UMontreal.CA> To: chemistry@www.ccl.net From: Dennis.Salahub@UMontreal.CA (Dennis Salahub) X-Sender: salahub@poste.umontreal.ca Subject: NATO-ASI Metal-ligand Interactions, Cetraro, Italy, Sep. 1-13 Cc: nrusso@unical.it NATO Advanced Study Institute Metal-Ligand Interactions in Chemistry, Physics and Biology Cetraro, Calabria, Italy Sept 1 - 13, 1998 Lecturers: Gernot Frenking, Francesc Illas, Dennis Salahub, Nino Russo, Karlheinz Schwarz, Julius Jellinek, Ha-Jo Freund, Jacek Lipkowski, Fritz Siebert, Peter Hackett, Bernard Coq, Dave Case, Ivano Bertini and Ed Solomon. There will also be several Special Research Seminars and a poster session. Web site: http://ccumc1.unical.it/scuole/nato-asi-mli/ Application,further information: Professor Nino Russo, nrusso@unical.it From pwalters@vpharm.com Thu Apr 9 20:23:34 1998 Received: from fringe.vpharm.com for pwalters@vpharm.com by www.ccl.net (8.8.3/950822.1) id TAA27534; Thu, 9 Apr 1998 19:43:37 -0400 (EDT) Received: from vpharm.com by fringe.vpharm.com via smtpd (for www.ccl.net [192.148.249.5]) with SMTP; 9 Apr 1998 23:43:37 UT Received: from vpharm.com (as5200-ppp-3.vpharm.com [10.8.1.52]) by portal.vpharm.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id TAA25884 for ; Thu, 9 Apr 1998 19:41:44 -0400 Sender: pat@portal.vpharm.com Message-ID: <352D576D.2FC645F9@vpharm.com> Date: Thu, 09 Apr 1998 19:19:09 -0400 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 4.04 [en] (X11; I; Linux 2.0.0 i586) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: De Novo Ligand Design - Boston ACS Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit ===== CALL FOR PAPERS ===== Session on De Novo Ligand Design American Chemical Society Meeting Boston, MA, August, 1998 I am looking for papers (both oral presentations and posters) on the subject of the design and use of ligand design software. Previously unpublished methods, as well as novel applications of de novo methods, are especially welcome. If you would like to present a talk or a poster at this session, please send email to pwalters@vpharm.com. The abstract deadline is April 19, so please contact me ASAP. -- W. Patrick Walters, Ph.D. Senior Staff Investigator, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6442 FAX: (617)577-6400