From chemistry-request@server.ccl.net Wed Mar 1 18:08:43 2000 Received: from mtiwmhc25.worldnet.att.net (imail@mtiwmhc25.worldnet.att.net [204.127.131.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA08268 for ; Wed, 1 Mar 2000 18:08:43 -0500 Received: from nt ([12.67.2.254]) by mtiwmhc25.worldnet.att.net (InterMail vM.4.01.02.31a 201-229-119-114) with ESMTP id <20000301230747.IBXC17940.mtiwmhc25.worldnet.att.net@nt> for ; Wed, 1 Mar 2000 23:07:47 +0000 Message-Id: <4.2.0.58.20000301154206.00ad3d90@postoffice.worldnet.att.net> X-Sender: mrmopac@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Wed, 01 Mar 2000 15:42:06 -0700 To: chemistry@ccl.net From: "James J. P. Stewart" Subject: AM1 and PM3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Although regarded by many as unqualified to offer a review of AM1 and PM3, by reason of presumed bias, I nevertheless feel that some factual input on this topic would be useful. For a list of known faults, average errors in heats of formation, geometries, etc. in MNDO, AM1, and PM3, please look in http://www.schrodinger.com/Mopac/html/node656.html or http://home.att.net/~mopacmanual/node656.html My objective in writing AM1 and PM3 was to reduce the error in computed quantities, including hydrogen bonds. This was partly successful in AM1 - the geometry of the water dimer was incorrect, and partly successful in PM3 - the shape of the PES was incorrect. Jimmy Stewart ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart@fujitsu.com | | 15210 Paddington Circle | WWW: http://home.att.net/~MrMOPAC | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From chemistry-request@server.ccl.net Thu Mar 2 00:21:01 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA09588 for ; Thu, 2 Mar 2000 00:20:59 -0500 Received: from unipune.ernet.in (unipune.unipune.ernet.in [196.1.114.75]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id KAA01698 for ; Thu, 2 Mar 2000 10:40:09 +0530 Received: (from gadre@localhost) by unipune.ernet.in (8.9.0/UnipuneV1.2) id LAA28926 for CHEMISTRY@www.ccl.net; Thu, 2 Mar 2000 11:07:57 +0530 Date: Thu, 2 Mar 2000 11:07:57 +0530 From: "Prof. S. R. Gadre Faculty member" Message-Id: <200003020537.LAA28926@unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: PPP Dear Sirs and Madams : Pl. send me a source from which I could get the fortran source code for a PPP program. Thanks in advance..........Selina From chemistry-request@server.ccl.net Thu Mar 2 04:29:48 2000 Received: from kmucc.keimyung.ac.kr ([203.247.29.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA10539 for ; Thu, 2 Mar 2000 04:29:45 -0500 Received: from SIMUL1 (simul-1.keimyung.ac.kr [203.247.7.49]) by kmucc.keimyung.ac.kr (8.9.3-H/8.9.3) with SMTP id SAA00192 for ; Thu, 2 Mar 2000 18:19:05 +0900 (KST) Message-ID: <001001bf8429$19990ed0$3107f7cb@SIMUL1> From: "Viorel Chihaia" To: Subject: UNIX <--> DOS <--> MAC conversion files Date: Thu, 2 Mar 2000 18:24:24 +0900 There are different programs for UNIX <--> DOS <--> MAC conversion = files. Take a look at these www pages: http://www.tamasoft.co.jp/freesoft/cvret-e.html http://www.ctyme.com/cleantxt.html or http://citforum.ints.net/operating_systems/manpages/UNIX2DOS.1.shtml Viorel From chemistry-request@server.ccl.net Thu Mar 2 07:48:44 2000 Received: from mtiwmhc27.worldnet.att.net (imail@mtiwmhc27.worldnet.att.net [204.127.131.52]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA12126 for ; Thu, 2 Mar 2000 07:48:43 -0500 Received: from dell ([63.30.47.169]) by mtiwmhc27.worldnet.att.net (InterMail vM.4.01.02.31a 201-229-119-114) with SMTP id <20000302124729.BRAG24363.mtiwmhc27.worldnet.att.net@dell>; Thu, 2 Mar 2000 12:47:29 +0000 Message-Id: <3.0.6.32.20000302044711.009a9d50@postoffice.worldnet.att.net> X-Sender: davidgallagher@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 02 Mar 2000 04:47:11 -0800 To: elewars From: David Gallagher Subject: Re: SEMIEMPIRICAL REVIEWS Cc: chemistry@ccl.net In-Reply-To: <38BD4F82.4CAD4C@trentu.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id HAA12127 In case anyone is interested, Jimmy Stewart, author of MOPAC, will be talking about the evolution of semi-empirical codes and the latest developments in MOPAC at the MOPAC User Group meeting at the ACS, Saturday 25th March 1.30pm, Argent Hotel, 50 Third Street, San Francisco. Details are available at http://www.schrodinger.com/Forms/mopac_ugm.html David Gallagher Fujitsu At 12:12 PM 3/1/00 -0500, elewars wrote: >Wed, 2000 March 1 > >Here is the summary of the answers I received to my question about >recent reviews of semiempirical methods. Thanks very much to all who >responded. > EL >===== > >The Question > >Friday Feb 25 > >Hello, > >If anyone knows of a *recent* (1995 or later) review of semiempirical >methods, including or devoted to AM1 and PM3, I would appreciate >receiving the reference. >(I looked in the CCL archives first; no luck). > >Thanks very much, >EL >====== >The Responses (#1--#8) > >#1 > >One of the books which accompanies Spartan has a discussion of >semi-empirical methods and a significant amount of data comparing them >to >other methods. Unfortunately, I do not think this book is readily >available. Here is the reference anyway: > >@Book{Hehre1998, > author = {Hehre, Warren J. and Yu, Jianguo and Klunzinger, > Philip E. and Lou, Liang}, > title = {A Brief Guide to Molecular Mechanics and Quantum > Chemical Calculations}, > publisher = {Wavefunction Inc.}, > year = 1998, > annote = {accompanied Spartan program - good overview, > ISBN 1-890661-05-8} > > Good luck - ned > Ned C. Haubein > Graduate Student > Dept. of Chemical Engineering > Northwestern University > 2145 Sheridan Rd / Rm E136 > Evanston, IL 60208-3120 > Phone: 847-467-1402 > Fax: 847-491-3728 > Email: n-haubein@nwu.edu > >= >#2 > >Did you consult the "Encyclopedia of Computational Chemistry"? >There are several articles about semiempirical topics including one >devoted to PM3 and one about AM1. > >Good luck, >Matthias > > >--------------------------------------------------------------------------- > > Dr. Matthias Hofmann > Anorganisch-Chemisches Institut > Ruprecht-Karls Universität Heidelberg Tel.: (INT+) 6221 >54-8451 > In Neuenheimer Feld 270 Fax.: (INT+) 6221 >54-8439 > D-69120 Heidelberg > Germany e-mail: >matthias.hofmann@urz.uni-heidelberg.de > >------------------------------------------------------------------------- > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >=========== > #3 > > Damien Laage > To: elewars >Hello, > >Could you please send me a copy of the answers you get? >Thank you very much, > >D. Laage >========= >#4 > >Hi, > >try: M.C. Zerner, Semiempirical molecular orbital methods, i.e. chapter >8 in >K.B. Lipkowitz, D.B. Boyd, Reviews in computational chemistry II >(VCH, NY, 1994, p. 313) > >Serge > _________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > tel(direct): 011/268315 > fax : 011/268301 > email : sergiusz.kwasniewski@luc.ac.be > _________________________________________________ >========== >#5 > >Could you, please, summarize answers? > >Best regards, > Mike mailto:mike@mnc.md > >=========== >#6 > > From: > David Young > To: elewars > >Try the Encylopedia of Computational Chemistry, John Wiley & Sons >(1998). > > Dave Young > youngd2@mail.auburn.edu > >------------------------------------------------------------------------ > > Live long and maintain marketable job skills. > >------------------------------------------------------------------------ > >============= >#7 > >Dear E. Lewars, > >I am sorry that I don't have a suggested reference at the moment, but I >would be very interested in knowning about these references as well. >Would >you please forward suggestions to me? > >I have been using MOPAC/PM3 and at a recent meeting someone blasted me >telling me how bad PM3 was for hydrogen bonding and asked my why I was >bothering to use it. I am planning on looking into this myself to get >an >idea on how bad/good it is - from other reading I have had the >impression >that PM3 was one of the best semi-empirical parameters sets to use for >energy values. I will email you any reviews that I find related to this >as >well. > >Thanks very much, >Bob Latour > > >Robert A. Latour Jr., Ph.D. >Associate Professor of Bioengineering > and Materials Science & Engineering >501 Rhodes Research Center >Clemson University, Clemson, SC 29634 >robert.latour@ces.clemson.edu >tel: (864) 656 -5552 / fax: (864) 656-4466 >============ >#8 > >Hello E. Lewars, > >Here is an article of your interest, > >''Some difficulties encountered with AM1 and PM3 calculations.'' >Tetrahedron, 54 (1998) 12841-12852 > >Gloria > >Dr. Gloria Ines Cardenas-Jiron >============================== >Departamento de Quimica de los Materiales, >Facultad de Quimica y Biologia, >Universidad de Santiago de Chile, >Casilla 40 Correo 33, Santiago, CHILE. > >Fax: (56-2) 681.2108 >Phone: (56-2) 681.2575 >============== > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Mar 2 14:47:42 2000 Received: from uscmail.usc.es (uscmail-atm.usc.es [193.144.78.21]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA02104 for ; Thu, 2 Mar 2000 14:47:33 -0500 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id TAA09229 for ; Thu, 2 Mar 2000 19:42:20 +0100 (MET) From: "Armando Navarro" To: Subject: Gaussian98w and SMP processing Date: Thu, 2 Mar 2000 19:34:28 +0100 Message-ID: <01bf8475$f183ccd0$eb4a90c1@qogolem.usc.es> Dear members: I have a Dual PentiumII PC and after installing PC-GAMESS I gave to the system variable named MKL_NPROC the value 2 in order to run GAMESS in SMP parallel mode. However I noticed a strange behavior of Gaussian98w after this. The program seems to use the two CPU, so I thought that Gaussian was effectively running in SMP mode. But when I measured the cpu and wall-clock times there was non improvement respect to set MKL_NPROC=3D1. Has anybody noticed this behavior of Gaussian in Dual Boxes? Regards Armando Navarro Departamento de quimica Organica Facultade de quimica Universidade de Santiago de Compostela Spain e-mail: qoajnv@usc.es From chemistry-request@server.ccl.net Thu Mar 2 12:29:38 2000 Received: from kodakr.kodak.com (kodakr.kodak.com [192.232.119.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA01542 for ; Thu, 2 Mar 2000 12:29:38 -0500 From: john.reinert-nash@kodak.com Received: from knotes.kodak.com (knotes2.kodak.com [150.221.122.53]) by kodakr.kodak.com (8.9.1/8.9.1) with SMTP id LAA00088 for ; Thu, 2 Mar 2000 11:25:19 -0500 (EST) Received: by knotes.kodak.com(Lotus SMTP MTA v4.6.2 (693.3 8-11-1998)) id 85256896.005A1620 ; Thu, 2 Mar 2000 11:23:58 -0500 X-Lotus-FromDomain: KODAK@INTERNET To: CHEMISTRY@ccl.net Message-ID: <85256896.005A14C0.00@knotes.kodak.com> Date: Thu, 2 Mar 2000 11:25:23 -0500 Subject: UNIX <--> DOS <--> MAC conversion files Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline From: John Reinert Nash@KODAK on 03/02/2000 11:25 AM To: CHEMISTRY@ccl.net@internet cc: Subject: UNIX <--> DOS <--> MAC conversion files On the subject of linefeed conversions, the program BBEdit (and BBEdit Lite) handles Mac<->PC<->Unix very easily and powerfully. The lite version is free. I found it very handy for editting g9x input files and dealing with various Unix output files on the Mac. relevant link: http://www.barebones.com/ John Reinert Nash jrnash@kodak.com Eastman Kodak Company 1/59/RL, Mailcode 01707 Rochester, NY 14650-1707 From chemistry-request@server.ccl.net Thu Mar 2 17:02:47 2000 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA03103 for ; Thu, 2 Mar 2000 17:02:44 -0500 Received: from ras20.icp.rssi.ru ( [194.85.223.61] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Thu, 2 Mar 2000 23:56:24 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-ID: <002101bf8489$f0daf290$3ddf55c2@alex> From: "Alex. A. Granovsky" To: References: <01bf8475$f183ccd0$eb4a90c1@qogolem.usc.es> Subject: Re: CCL:Gaussian98w and SMP processing Date: Thu, 2 Mar 2000 23:57:36 +0300 Organization: MSU MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Armando, > Dear members: > I have a Dual PentiumII PC and after installing PC-GAMESS I gave to the > system variable named MKL_NPROC the value 2 in order to run GAMESS in > SMP parallel mode. > However I noticed a strange behavior of Gaussian98w after this. The > program seems to use the two CPU, so I thought that Gaussian was > effectively running in SMP mode. > But when I measured the cpu and wall-clock times there was non > improvement respect to set MKL_NPROC=1. > Has anybody noticed this behavior of Gaussian in Dual Boxes? > Regards > Armando Navarro It seems that G98w uses old MKL v. 2.0 (or v. 2.1, I'm not sure) so it is affected by the MKL_NPROCS environment variable. The itself problem is in the MKL v. 2.0/2.1 behavior. Namely, the additional thread(s) are not suspended after matrix-matrix multiplication. Thus, G98w consumes CPU time on all CPUs, while the actual calculations are mainly performed only on one CPU. Next, it seems that the average size of matrices used by the G98w is relatively small, so there is no benefit due to usage of second CPU even if performing matrix-matrix multiplication. As to the PC GAMESS, we developed a workaround for this problem when dealing with old MKL 2.0. Starting from the MKL 3.0, the behavior of MKL-created threads was fixed, namely, they are suspended if not needed for actual calculations. Also, if you use PC GAMESS v. 5.3 and higher, the simplest way to set the number of CPUs used is simply set integer variable "mklnp" in $system group to the desired number of CPUs (it is longer not necessary to use MKL_NPROCS with the newer PC GAMESS). Best regards, Alex Granovsky From chemistry-request@server.ccl.net Thu Mar 2 17:22:26 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA03216 for ; Thu, 2 Mar 2000 17:22:26 -0500 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id NAA16373; Thu, 2 Mar 2000 13:18:06 -0800 (PST) Message-Id: <4.2.0.58.20000302133036.00abdb90@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 02 Mar 2000 13:31:14 -0800 To: "Armando Navarro" , From: Laurence Lavelle Subject: Re: CCL:Gaussian98w and SMP processing In-Reply-To: <01bf8475$f183ccd0$eb4a90c1@qogolem.usc.es> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed G98W does not use SMP. What your seeing is the OS using one CPU for all system management and G98W running on the other. My guess is about 20% CPU1 and 100% CPU2 respectively. Yes, it would be nice if G98W ran in SMP mode. Hope that helps. At 07:34 PM 03/02/2000 +0100, Armando Navarro wrote: >Dear members: >I have a Dual PentiumII PC and after installing PC-GAMESS I gave to the >system variable named MKL_NPROC the value 2 in order to run GAMESS in >SMP parallel mode. >However I noticed a strange behavior of Gaussian98w after this. The >program seems to use the two CPU, so I thought that Gaussian was >effectively running in SMP mode. >But when I measured the cpu and wall-clock times there was non >improvement respect to set MKL_NPROC=3D1. >Has anybody noticed this behavior of Gaussian in Dual Boxes? >Regards >Armando Navarro >Departamento de quimica Organica >Facultade de quimica >Universidade de Santiago de Compostela >Spain >e-mail: qoajnv@usc.es > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """"""""""""""""